Author: Pranav Ballaney Last-Update: 2020-05-14 02:52:25 +0530 Description: Test results to compare with are just wrong as discussed with upstream See https://lists.debian.org/debian-med/2020/05/msg00118.html --- a/tests/check-cons-pure-prot +++ b/tests/check-cons-pure-prot @@ -15,10 +15,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) @@ -48,16 +74,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -72,20 +98,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -159,23 +186,23 @@ BIPARTITIONS The following bipartitions occured at least once in the specified set of 100 usertrees tree topologies. Bipartitions included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 100 - ****... : 100 - **..... : 100 + **..*** : 100 (1.000) + ****... : 100 (1.000) + **..... : 100 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****..* : 40 + ****..* : 40 (0.400) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 37 - ****.*. : 23 + *****.. : 37 (0.370) + ****.*. : 23 (0.230) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) --- a/tests/check-lm-pure-prot +++ b/tests/check-lm-pure-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -132,43 +159,86 @@ Sequences are not grouped in clusters. LIKELIHOOD MAPPING STATISTICS -Occupancies of the three areas 1, 2, 3: + (a,b)-(c,d) (a,b)-(c,d) + /\ /\ + / \ / \ + / \ / 1 \ + / a1 \ / \ / \ + /\ /\ / \/ \ + / \ / \ / /\ \ + / \ / \ / 6 / \ 4 \ + / \/ \ /\ / 7 \ /\ + / | \ / \ /______\ / \ + / a3 | a2 \ / 3 | 5 | 2 \ + /__________|_________\ /_____|________|_____\ +(a,d)-(b,c) (a,c)-(b,d) (a,b)-(c,d) (a,c)-(b,d) + + +For more information about likelihood-mapping refer to + Strimmer and von Haeseler (1997) PNAS 94:6815-6819 +and/or + Schmidt and von Haeseler (2003) Current Protocols in Bioinformatics + (by Baxevanis et al., Eds.), Unit 6, Wiley&Sons, New York. + + + + +Quartet support of regions a1, a2, a3: + + name #quartets a1 (% a1) a2 (% a2) a3 (% a3) +----------------------------------------------------------------------------- + 1 HBB_HUMAN 20 6 ( 30.00) 5 ( 25.00) 9 ( 45.00) + 2 HBB_HORSE 20 6 ( 30.00) 7 ( 35.00) 7 ( 35.00) + 3 HBA_HUMAN 20 6 ( 30.00) 5 ( 25.00) 9 ( 45.00) + 4 HBA_HORSE 20 7 ( 35.00) 4 ( 20.00) 9 ( 45.00) + 5 MYG_PHYCA 20 5 ( 25.00) 7 ( 35.00) 8 ( 40.00) + 6 GLB5_PETMA 20 10 ( 50.00) 3 ( 15.00) 7 ( 35.00) + 7 LGB2_LUPLU 20 8 ( 40.00) 5 ( 25.00) 7 ( 35.00) +----------------------------------------------------------------------------- + 35 12 ( 34.29) 9 ( 25.71) 14 ( 40.00) + + + +Quartet support of areas 1-7: + + resolved partly unresolved + name #quartets 1 (% 1) 2 (% 2) 3 (% 3) 4 (% 4) 5 (% 5) 6 (% 6) 7 (% 7) +------------------------------------------------------------------------------------------------------------------------------------------------- + 1 HBB_HUMAN 20 6 ( 30.00) 5 ( 25.00) 8 ( 40.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 1 ( 5.00) + 2 HBB_HORSE 20 6 ( 30.00) 7 ( 35.00) 7 ( 35.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) + 3 HBA_HUMAN 20 5 ( 25.00) 5 ( 25.00) 9 ( 45.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 1 ( 5.00) + 4 HBA_HORSE 20 7 ( 35.00) 4 ( 20.00) 8 ( 40.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 1 ( 5.00) + 5 MYG_PHYCA 20 4 ( 20.00) 7 ( 35.00) 6 ( 30.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 3 ( 15.00) + 6 GLB5_PETMA 20 9 ( 45.00) 3 ( 15.00) 5 ( 25.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 3 ( 15.00) + 7 LGB2_LUPLU 20 7 ( 35.00) 5 ( 25.00) 5 ( 25.00) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 3 ( 15.00) +------------------------------------------------------------------------------------------------------------------------------------------------- + 35 11 ( 31.43) 9 ( 25.71) 12 ( 34.29) 0 ( 0.00) 0 ( 0.00) 0 ( 0.00) 3 ( 8.57) + + + +Quartet resolution per sequence: + + + + name #quartets resolved partly unresolved +----------------------------------------------------------------------------- + 1 HBB_HUMAN 20 19 ( 95.00) 0 ( 0.00) 1 ( 5.00) + 2 HBB_HORSE 20 20 (100.00) 0 ( 0.00) 0 ( 0.00) + 3 HBA_HUMAN 20 19 ( 95.00) 0 ( 0.00) 1 ( 5.00) + 4 HBA_HORSE 20 19 ( 95.00) 0 ( 0.00) 1 ( 5.00) + 5 MYG_PHYCA 20 17 ( 85.00) 0 ( 0.00) 3 ( 15.00) + 6 GLB5_PETMA 20 17 ( 85.00) 0 ( 0.00) 3 ( 15.00) + 7 LGB2_LUPLU 20 17 ( 85.00) 0 ( 0.00) 3 ( 15.00) +----------------------------------------------------------------------------- + 35 32 ( 91.43) 0 ( 0.00) 3 ( 8.57) + + + +Overall quartet resolution: - /\ - / \ - / \ - / 1 \ - / \ / \ - / \ / \ - / \/ \ - / 3 : 2 \ - / : \ - /__________________\ - -Number of quartets in region 1: 14 (= 40.0%) -Number of quartets in region 2: 11 (= 31.4%) -Number of quartets in region 3: 10 (= 28.6%) - -Occupancies of the seven areas 1, 2, 3, 4, 5, 6, 7: - - /\ - / \ - / 1 \ - / \ / \ - / /\ \ - / 6 / \ 4 \ - / / 7 \ \ - / \ /______\ / \ - / 3 : 5 : 2 \ - /__________________\ - -Number of quartets in region 1: 12 (= 34.3%) left: 3 right: 9 -Number of quartets in region 2: 11 (= 31.4%) bottom: 3 top: 8 -Number of quartets in region 3: 9 (= 25.7%) bottom: 4 top: 5 -Number of quartets in region 4: 0 (= 0.0%) bottom: 0 top: 0 -Number of quartets in region 5: 0 (= 0.0%) left: 0 right: 0 -Number of quartets in region 6: 0 (= 0.0%) bottom: 0 top: 0 -Number of quartets in region 7: 3 (= 8.6%) +Number of resolved quartets (regions 1+2+3): 32 (= 91.43%) +Number of partly resolved quartets (regions 4+5+6): 0 (= 0.00%) +Number of unresolved quartets (region 7): 3 (= 8.57%) TIME STAMP --- a/tests/check-qp-clock +++ b/tests/check-qp-clock @@ -14,10 +14,37 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) @@ -45,17 +72,17 @@ Expected pyrimidine transition/purine tr AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -70,18 +97,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -98,19 +126,19 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 +Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 -Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 +Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 -Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 +Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 -Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 +Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 @@ -128,18 +156,18 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 - Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 - Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 - Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 - Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 - Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 - Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 - Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 + 2 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 + 3 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 + 4 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + 5 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 + 6 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 + 7 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 + 8 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- - #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 + #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -182,15 +210,15 @@ This quartet puzzling tree is not comple :---Trichosuru - :-----97: + :----100: : :---Phalanger : : :---Sarcophilu - : :-98: + : :100: : : :---Dasyurus : : - :-71: :---Philander - : :-65: + :-73: :---Philander + : :-71: : : :---Bos : : : :-------Echymipera @@ -200,8 +228,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, -(Philander,Bos)65,Echymipera)71); +(Thylacinus,(Trichosuru,Phalanger)100,((Sarcophilu,Dasyurus)100, +(Philander,Bos)71,Echymipera)73); BIPARTITIONS @@ -209,44 +237,44 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 981 - ****..** : 971 - *...**.. : 713 - ******.. : 649 + ****..** : 999 (0.999) + *..***** : 999 (0.999) + *...**.. : 730 (0.730) + ******.. : 711 (0.711) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 426 + *...**** : 466 (0.466) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 347 - ***.**.* : 150 - *...**.* : 131 - *..***.. : 87 - *..*..** : 81 - *.....** : 72 - ****..*. : 55 - ***.***. : 37 - ****.... : 36 - *..***.* : 36 - ***..... : 31 - *.....*. : 28 - *...***. : 27 - *......* : 27 - *....*.. : 26 - *..*.... : 21 - **..**** : 16 - ***...** : 14 - *..*..*. : 13 - *..****. : 12 + ***.**.. : 333 (0.333) + *...**.* : 171 (0.171) + ***.**.* : 89 (0.089) + *..***.. : 80 (0.080) + *.....** : 79 (0.079) + *..*..** : 69 (0.069) + ****..*. : 51 (0.051) + *......* : 34 (0.034) + *..***.* : 30 (0.030) + ****.... : 28 (0.028) + ***.***. : 27 (0.027) + *..*.... : 22 (0.022) + *...***. : 20 (0.020) + ***..... : 19 (0.019) + *.....*. : 14 (0.014) + *..****. : 9 (0.009) + *..*..*. : 8 (0.008) + ***...** : 6 (0.006) + ***....* : 4 (0.004) + ****.**. : 1 (0.001) -(6 other less frequent bipartitions not shown) +(1 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -275,7 +303,7 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 -Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 +Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 @@ -286,9 +314,9 @@ Bos 8 0.13479 0.04095 lo Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, -((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, -Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); +(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953, +((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995, +Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -343,9 +371,9 @@ Bos 8 0.09549 1.412 lo Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 -,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, -Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); +(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)100:0.04504 +,((Sarcophilu:0.06189,Dasyurus:0.06189)100:0.06663,(Philander:0.09549, +Bos:0.09549)71:0.03304,Echymipera:0.12852)73:0.01851):0.00001); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-hky-clock-nucl +++ b/tests/check-qp-hky-clock-nucl @@ -14,10 +14,37 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) @@ -45,17 +72,17 @@ Expected pyrimidine transition/purine tr AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -70,18 +97,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -98,19 +126,19 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 +Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 -Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 +Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 -Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 +Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 -Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 +Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 @@ -128,18 +156,18 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 - Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 - Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 - Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 - Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 - Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 - Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 - Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 + 2 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 + 3 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 + 4 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + 5 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 + 6 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 + 7 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 + 8 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- - #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 + #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -182,15 +210,15 @@ This quartet puzzling tree is not comple :---Trichosuru - :-----97: + :----100: : :---Phalanger : : :---Sarcophilu - : :-98: + : :100: : : :---Dasyurus : : - :-71: :---Philander - : :-65: + :-73: :---Philander + : :-71: : : :---Bos : : : :-------Echymipera @@ -200,8 +228,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, -(Philander,Bos)65,Echymipera)71); +(Thylacinus,(Trichosuru,Phalanger)100,((Sarcophilu,Dasyurus)100, +(Philander,Bos)71,Echymipera)73); BIPARTITIONS @@ -209,44 +237,44 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 981 - ****..** : 971 - *...**.. : 713 - ******.. : 649 + ****..** : 999 (0.999) + *..***** : 999 (0.999) + *...**.. : 730 (0.730) + ******.. : 711 (0.711) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 426 + *...**** : 466 (0.466) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 347 - ***.**.* : 150 - *...**.* : 131 - *..***.. : 87 - *..*..** : 81 - *.....** : 72 - ****..*. : 55 - ***.***. : 37 - ****.... : 36 - *..***.* : 36 - ***..... : 31 - *.....*. : 28 - *...***. : 27 - *......* : 27 - *....*.. : 26 - *..*.... : 21 - **..**** : 16 - ***...** : 14 - *..*..*. : 13 - *..****. : 12 + ***.**.. : 333 (0.333) + *...**.* : 171 (0.171) + ***.**.* : 89 (0.089) + *..***.. : 80 (0.080) + *.....** : 79 (0.079) + *..*..** : 69 (0.069) + ****..*. : 51 (0.051) + *......* : 34 (0.034) + *..***.* : 30 (0.030) + ****.... : 28 (0.028) + ***.***. : 27 (0.027) + *..*.... : 22 (0.022) + *...***. : 20 (0.020) + ***..... : 19 (0.019) + *.....*. : 14 (0.014) + *..****. : 9 (0.009) + *..*..*. : 8 (0.008) + ***...** : 6 (0.006) + ***....* : 4 (0.004) + ****.**. : 1 (0.001) -(6 other less frequent bipartitions not shown) +(1 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -275,7 +303,7 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 -Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 +Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 @@ -286,9 +314,9 @@ Bos 8 0.13479 0.04095 lo Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, -((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, -Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); +(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953, +((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995, +Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -343,9 +371,9 @@ Bos 8 0.09549 1.412 lo Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 -,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, -Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); +(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)100:0.04504 +,((Sarcophilu:0.06189,Dasyurus:0.06189)100:0.06663,(Philander:0.09549, +Bos:0.09549)71:0.03304,Echymipera:0.12852)73:0.01851):0.00001); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-hky-rhet-clock-nucl +++ b/tests/check-qp-hky-rhet-clock-nucl @@ -14,22 +14,49 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) -Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) +Transition/transversion parameter (estimated from data set): 2.43 (S.E. 0.84) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 - A-G rate: 5.85063 + A-G rate: 4.86122 A-T rate: 1.00000 C-G rate: 1.00000 - C-T rate: 5.85063 + C-T rate: 4.86122 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): @@ -39,23 +66,23 @@ Nucleotide frequencies (estimated from d pi(G) = 12.0% pi(T) = 30.7% -Expected transition/transversion ratio: 3.14 +Expected transition/transversion ratio: 2.59 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -70,18 +97,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -98,73 +126,69 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.52940 0.37900 0.36 0.58922 0.56150 0.43932 - 0.91 -Sarcophilu 0.52940 0.00000 0.17837 0.62 0.69892 0.93602 0.62327 - 0.78596 -Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 - 0.20 -Echymipera 0.36 0.62 0.39032 0.00000 0.70229 0.94283 0.42016 - 0.66063 -Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 - 0.62697 -Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 - 0.98921 -Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 - 0.49264 -Bos 0.91 0.78596 0.20 0.66063 0.62697 0.98921 0.49264 +Thylacinus 0.00000 0.43053 0.31881 0.42777 0.48001 0.46047 0.36257 + 0.45946 +Sarcophilu 0.43053 0.00000 0.16226 0.50810 0.56683 0.75575 0.50979 + 0.63867 +Dasyurus 0.31881 0.16226 0.00000 0.32754 0.43706 0.49686 0.26949 + 0.46769 +Echymipera 0.42777 0.50810 0.32754 0.00000 0.56231 0.75320 0.35005 + 0.54053 +Trichosuru 0.48001 0.56683 0.43706 0.56231 0.00000 0.32946 0.56635 + 0.51026 +Phalanger 0.46047 0.75575 0.49686 0.75320 0.32946 0.00000 0.64553 + 0.79725 +Philander 0.36257 0.50979 0.26949 0.35005 0.56635 0.64553 0.00000 + 0.40838 +Bos 0.45946 0.63867 0.46769 0.54053 0.51026 0.79725 0.40838 0.00000 -Average distance (over all possible pairs of sequences): 0.59096 - minimum : 0.17837, maximum : 0.98921 - variance : 0.03581, std.dev. : 0.18924 +Average distance (over all possible pairs of sequences): 0.48368 + minimum : 0.16226, maximum : 0.79725 + variance : 0.02195, std.dev. : 0.14817 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates -Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) -Number of Gamma rate categories: 8 +Gamma distribution parameter alpha (estimated from data set): 0.26 (S.E. 0.05) +Number of Gamma rate categories: 4 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.0000 0.1250 - 2 0.0031 0.1250 - 3 0.0262 0.1250 - 4 0.1071 0.1250 - 5 0.3140 0.1250 - 6 0.7768 0.1250 - 7 1.8180 0.1250 - 8 4.9547 0.1250 + 1 0.0007 0.2500 + 2 0.0674 0.2500 + 3 0.5911 0.2500 + 4 3.3407 0.2500 -Categories 1-8 approximate a continous Gamma-distribution with expectation 1 -and variance 3.94. +Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 +and variance 3.91. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): - 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 - 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 - 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 - 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 + 4 1 1 4 1 1 4 1 1 4 4 1 4 4 1 3 1 1 4 4 1 4 1 1 1 4 1 1 4 3 + 4 3 1 4 1 1 1 1 1 3 3 1 4 1 1 3 1 1 4 3 1 1 1 1 4 4 1 1 1 1 + 4 1 1 3 1 1 4 1 1 3 1 1 4 4 1 4 1 1 3 1 1 3 4 4 4 1 1 4 1 1 + 4 1 1 4 1 1 4 1 1 4 3 1 4 3 1 4 1 1 4 1 1 4 1 3 4 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 - Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 - Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 - Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 - Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 - Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 - Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 - Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 + 2 Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 + 3 Dasyurus 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 + 4 Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 + 5 Trichosuru 17 [ 48.57%] 1 [ 2.86%] 17 [ 48.57%] 35 + 6 Phalanger 21 [ 60.00%] 1 [ 2.86%] 13 [ 37.14%] 35 + 7 Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 + 8 Bos 10 [ 28.57%] 2 [ 5.71%] 23 [ 65.71%] 35 -------------------------------------------------------------------------- - #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 + #quartets : 31 [ 44.29%] 2 [ 2.86%] 37 [ 52.86%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -190,8 +214,8 @@ and to simultaneously infer support valu Number of puzzling steps: 1000 Analysed quartets: 70 -Fully resolved quartets: 30 (= 42.9%) -Partly resolved quartets: 3 (= 4.3%) +Fully resolved quartets: 31 (= 44.3%) +Partly resolved quartets: 2 (= 2.9%) Unresolved quartets: 37 (= 52.9%) Quartet trees are based on approximate maximum likelihood values @@ -206,27 +230,27 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---Sarcophilu - :-90: - : :---Dasyurus - : - : :---Trichosuru - :-87: - : :---Phalanger - : - :-------Echymipera - : - :-------Philander - : - :-------Bos - : - :-------Thylacinus + :---Trichosuru + :-----98: + : :---Phalanger + : + : :---Sarcophilu + : :-97: + : : :---Dasyurus + : : + :-59:-------Echymipera + : : + : :-------Philander + : : + : :-------Bos + : + :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, -Echymipera,Philander,Bos); +(Thylacinus,(Trichosuru,Phalanger)98,((Sarcophilu,Dasyurus)97, +Echymipera,Philander,Bos)59); BIPARTITIONS @@ -234,43 +258,44 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 904 - ****..** : 872 + ****..** : 977 (0.977) + *..***** : 966 (0.966) + *...**.. : 591 (0.591) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**.. : 377 - ******.. : 357 + ***.**.* : 289 (0.289) + ***.**.. : 257 (0.257) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.* : 220 - ***.**.. : 218 - *...**** : 205 - ***.***. : 145 - *......* : 135 - *..*..** : 129 - *...**.* : 124 - *.....** : 106 - *..*.... : 102 - *..***.* : 92 - *..***.. : 91 - ***..... : 86 - *.....*. : 71 - ***...** : 70 - *..****. : 67 - ****..*. : 67 - *....*.. : 64 - *...***. : 54 - ****.... : 52 - *..*...* : 47 + ******.. : 256 (0.256) + ***.***. : 240 (0.240) + *...**** : 177 (0.177) + *...**.* : 148 (0.148) + *..***.* : 130 (0.130) + *..***.. : 102 (0.102) + *......* : 95 (0.095) + *..****. : 92 (0.092) + *...***. : 91 (0.091) + *..*..** : 82 (0.082) + ***..... : 70 (0.070) + ****..*. : 69 (0.069) + ****.... : 36 (0.036) + *..*.... : 36 (0.036) + *.....*. : 36 (0.036) + *.....** : 32 (0.032) + ***....* : 31 (0.031) + ***...** : 31 (0.031) + *..*...* : 26 (0.026) + *..*..*. : 26 (0.026) -(49 other less frequent bipartitions not shown) +(29 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -279,32 +304,32 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :------2 Sarcophilu - :-------9 - : :-3 Dasyurus - : - : :-----5 Trichosuru - :-------10 - : :--------6 Phalanger - : - :--------4 Echymipera - : - :-------7 Philander + :------5 Trichosuru + :------9 + : :-------6 Phalanger : - :-----------8 Bos + : :------2 Sarcophilu + : :------10 + : : :-3 Dasyurus + : : + : :-------4 Echymipera + :---11 + : :------7 Philander + : : + : :-----------8 Bos : - :-------1 Thylacinus + :-----1 Thylacinus branch length S.E. branch length S.E. -Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 -Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 -Dasyurus 3 0.00001 0.00200 -Echymipera 4 0.27841 0.11691 -Trichosuru 5 0.17822 0.10160 -Phalanger 6 0.27519 0.12613 -Philander 7 0.22533 0.10269 10 iterations until convergence -Bos 8 0.38507 0.14566 log L: -570.33 +Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889 +Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510 +Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178 +Echymipera 4 0.20360 0.08378 +Trichosuru 5 0.15345 0.07805 +Phalanger 6 0.18858 0.08736 +Philander 7 0.16082 0.07443 10 iterations until convergence +Bos 8 0.30632 0.12025 log L: -569.50 WARNING --- at least one branch length is close to an internal boundary! @@ -312,9 +337,9 @@ WARNING --- at least one branch length i Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, -(Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, -Philander:0.22533,Bos:0.38507); +(Thylacinus:0.13266,(Trichosuru:0.15345,Phalanger:0.18858)98:0.14146, +((Sarcophilu:0.16398,Dasyurus:0.00001)97:0.15536,Echymipera:0.20360, +Philander:0.16082,Bos:0.30632)59:0.07879); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -322,64 +347,65 @@ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CON Branch lengths are computed using the selected model of substitution and rate heterogeneity. -Root located at branch: 10 "internal branch" (automatic search) +Root located at branch: 9 "internal branch" (automatic search) If the automatic search misplaces the root please rerun the analysis (rename "outtree" to "intree") and select location of root manually! - :---2 Sarcophilu + :------5 Trichosuru :-------9 - : :---3 Dasyurus - : - : :-------5 Trichosuru - :-------10 - : :-------6 Phalanger - : - :---------4 Echymipera - : - :---------7 Philander + : :------6 Phalanger : - :---------8 Bos + : :---2 Sarcophilu + : :-----10 + : : :---3 Dasyurus + : : + : :--------4 Echymipera + :-11 + : :--------7 Philander + : : + : :--------8 Bos : - :---------1 Thylacinus + :--------1 Thylacinus Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) -Thylacinus 1 0.29776 0.785 9 0.20356 0.979 -Sarcophilu 2 0.09420 2.007 10 0.22846 0.976 -Dasyurus 3 0.09420 0.000 -Echymipera 4 0.29776 0.935 -Trichosuru 5 0.23472 0.759 -Phalanger 6 0.23472 1.172 -Philander 7 0.29776 0.757 16 iterations until convergence -Bos 8 0.29776 1.293 log L: -573.89 +Thylacinus 1 0.23195 0.572 9 0.16278 0.869 +Sarcophilu 2 0.07833 2.094 10 0.14771 1.052 +Dasyurus 3 0.07833 0.000 11 0.00592 13.307 +Echymipera 4 0.22603 0.901 +Trichosuru 5 0.17300 0.887 +Phalanger 6 0.17300 1.090 +Philander 7 0.22603 0.711 13 iterations until convergence +Bos 8 0.22603 1.355 log L: -574.14 height S.E. of node common to branches -0.23472 0.07631 10 5 6 -0.09420 0.03153 9 2 3 -0.29776 0.05401 10 4 7 8 1 9 -0.38047 0.07031 of root at branch 10 +0.17300 0.05161 9 5 6 +0.07833 0.02407 10 2 3 +0.22603 0.03673 11 10 4 7 8 +0.23195 0.04168 9 11 1 +0.28387 0.04995 of root at branch 9 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -((Trichosuru:0.23472,Phalanger:0.23472)87:0.14575,(Echymipera:0.29776, -Philander:0.29776,Bos:0.29776,Thylacinus:0.29776,(Sarcophilu:0.09420, -Dasyurus:0.09420)90:0.20356):0.08271); +((Trichosuru:0.17300,Phalanger:0.17300)98:0.11086,(((Sarcophilu:0.07833, +Dasyurus:0.07833)97:0.14771,Echymipera:0.22603,Philander:0.22603, +Bos:0.22603)59:0.00592,Thylacinus:0.23195):0.05191); MOLECULAR CLOCK LIKELIHOOD RATIO TEST -log L without clock: -570.33 (independent branch parameters: 10) -log L with clock: -573.89 (independent branch parameters: 4) +log L without clock: -569.50 (independent branch parameters: 11) +log L with clock: -574.14 (independent branch parameters: 5) -Likelihood ratio test statistic delta: 7.12 +Likelihood ratio test statistic delta: 9.26 Degress of freedom of chi-square distribution: 6 -Critical significance level: 30.97% +Critical significance level: 15.94% The simpler (clocklike) tree can not be rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree --- a/tests/check-qp-hky-rhet-nucl +++ b/tests/check-qp-hky-rhet-nucl @@ -14,22 +14,49 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) -Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) +Transition/transversion parameter (estimated from data set): 2.43 (S.E. 0.84) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 - A-G rate: 5.85063 + A-G rate: 4.86122 A-T rate: 1.00000 C-G rate: 1.00000 - C-T rate: 5.85063 + C-T rate: 4.86122 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): @@ -39,23 +66,23 @@ Nucleotide frequencies (estimated from d pi(G) = 12.0% pi(T) = 30.7% -Expected transition/transversion ratio: 3.14 +Expected transition/transversion ratio: 2.59 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -70,18 +97,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -98,73 +126,69 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.52940 0.37900 0.36 0.58922 0.56150 0.43932 - 0.91 -Sarcophilu 0.52940 0.00000 0.17837 0.62 0.69892 0.93602 0.62327 - 0.78596 -Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 - 0.20 -Echymipera 0.36 0.62 0.39032 0.00000 0.70229 0.94283 0.42016 - 0.66063 -Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 - 0.62697 -Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 - 0.98921 -Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 - 0.49264 -Bos 0.91 0.78596 0.20 0.66063 0.62697 0.98921 0.49264 +Thylacinus 0.00000 0.43053 0.31881 0.42777 0.48001 0.46047 0.36257 + 0.45946 +Sarcophilu 0.43053 0.00000 0.16226 0.50810 0.56683 0.75575 0.50979 + 0.63867 +Dasyurus 0.31881 0.16226 0.00000 0.32754 0.43706 0.49686 0.26949 + 0.46769 +Echymipera 0.42777 0.50810 0.32754 0.00000 0.56231 0.75320 0.35005 + 0.54053 +Trichosuru 0.48001 0.56683 0.43706 0.56231 0.00000 0.32946 0.56635 + 0.51026 +Phalanger 0.46047 0.75575 0.49686 0.75320 0.32946 0.00000 0.64553 + 0.79725 +Philander 0.36257 0.50979 0.26949 0.35005 0.56635 0.64553 0.00000 + 0.40838 +Bos 0.45946 0.63867 0.46769 0.54053 0.51026 0.79725 0.40838 0.00000 -Average distance (over all possible pairs of sequences): 0.59096 - minimum : 0.17837, maximum : 0.98921 - variance : 0.03581, std.dev. : 0.18924 +Average distance (over all possible pairs of sequences): 0.48368 + minimum : 0.16226, maximum : 0.79725 + variance : 0.02195, std.dev. : 0.14817 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates -Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) -Number of Gamma rate categories: 8 +Gamma distribution parameter alpha (estimated from data set): 0.26 (S.E. 0.05) +Number of Gamma rate categories: 4 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.0000 0.1250 - 2 0.0031 0.1250 - 3 0.0262 0.1250 - 4 0.1071 0.1250 - 5 0.3140 0.1250 - 6 0.7768 0.1250 - 7 1.8180 0.1250 - 8 4.9547 0.1250 + 1 0.0007 0.2500 + 2 0.0674 0.2500 + 3 0.5911 0.2500 + 4 3.3407 0.2500 -Categories 1-8 approximate a continous Gamma-distribution with expectation 1 -and variance 3.94. +Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 +and variance 3.91. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): - 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 - 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 - 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 - 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 + 4 1 1 4 1 1 4 1 1 4 4 1 4 4 1 3 1 1 4 4 1 4 1 1 1 4 1 1 4 3 + 4 3 1 4 1 1 1 1 1 3 3 1 4 1 1 3 1 1 4 3 1 1 1 1 4 4 1 1 1 1 + 4 1 1 3 1 1 4 1 1 3 1 1 4 4 1 4 1 1 3 1 1 3 4 4 4 1 1 4 1 1 + 4 1 1 4 1 1 4 1 1 4 3 1 4 3 1 4 1 1 4 1 1 4 1 3 4 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 - Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 - Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 - Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 - Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 - Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 - Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 - Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 + 2 Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 + 3 Dasyurus 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 + 4 Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 + 5 Trichosuru 17 [ 48.57%] 1 [ 2.86%] 17 [ 48.57%] 35 + 6 Phalanger 21 [ 60.00%] 1 [ 2.86%] 13 [ 37.14%] 35 + 7 Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 + 8 Bos 10 [ 28.57%] 2 [ 5.71%] 23 [ 65.71%] 35 -------------------------------------------------------------------------- - #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 + #quartets : 31 [ 44.29%] 2 [ 2.86%] 37 [ 52.86%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -190,8 +214,8 @@ and to simultaneously infer support valu Number of puzzling steps: 1000 Analysed quartets: 70 -Fully resolved quartets: 30 (= 42.9%) -Partly resolved quartets: 3 (= 4.3%) +Fully resolved quartets: 31 (= 44.3%) +Partly resolved quartets: 2 (= 2.9%) Unresolved quartets: 37 (= 52.9%) Quartet trees are based on approximate maximum likelihood values @@ -206,27 +230,27 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---Sarcophilu - :-90: - : :---Dasyurus - : - : :---Trichosuru - :-87: - : :---Phalanger - : - :-------Echymipera - : - :-------Philander - : - :-------Bos - : - :-------Thylacinus + :---Trichosuru + :-----98: + : :---Phalanger + : + : :---Sarcophilu + : :-97: + : : :---Dasyurus + : : + :-59:-------Echymipera + : : + : :-------Philander + : : + : :-------Bos + : + :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, -Echymipera,Philander,Bos); +(Thylacinus,(Trichosuru,Phalanger)98,((Sarcophilu,Dasyurus)97, +Echymipera,Philander,Bos)59); BIPARTITIONS @@ -234,43 +258,44 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 904 - ****..** : 872 + ****..** : 977 (0.977) + *..***** : 966 (0.966) + *...**.. : 591 (0.591) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**.. : 377 - ******.. : 357 + ***.**.* : 289 (0.289) + ***.**.. : 257 (0.257) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.* : 220 - ***.**.. : 218 - *...**** : 205 - ***.***. : 145 - *......* : 135 - *..*..** : 129 - *...**.* : 124 - *.....** : 106 - *..*.... : 102 - *..***.* : 92 - *..***.. : 91 - ***..... : 86 - *.....*. : 71 - ***...** : 70 - *..****. : 67 - ****..*. : 67 - *....*.. : 64 - *...***. : 54 - ****.... : 52 - *..*...* : 47 + ******.. : 256 (0.256) + ***.***. : 240 (0.240) + *...**** : 177 (0.177) + *...**.* : 148 (0.148) + *..***.* : 130 (0.130) + *..***.. : 102 (0.102) + *......* : 95 (0.095) + *..****. : 92 (0.092) + *...***. : 91 (0.091) + *..*..** : 82 (0.082) + ***..... : 70 (0.070) + ****..*. : 69 (0.069) + ****.... : 36 (0.036) + *..*.... : 36 (0.036) + *.....*. : 36 (0.036) + *.....** : 32 (0.032) + ***....* : 31 (0.031) + ***...** : 31 (0.031) + *..*...* : 26 (0.026) + *..*..*. : 26 (0.026) -(49 other less frequent bipartitions not shown) +(29 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -279,32 +304,32 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :------2 Sarcophilu - :-------9 - : :-3 Dasyurus - : - : :-----5 Trichosuru - :-------10 - : :--------6 Phalanger - : - :--------4 Echymipera - : - :-------7 Philander + :------5 Trichosuru + :------9 + : :-------6 Phalanger : - :-----------8 Bos + : :------2 Sarcophilu + : :------10 + : : :-3 Dasyurus + : : + : :-------4 Echymipera + :---11 + : :------7 Philander + : : + : :-----------8 Bos : - :-------1 Thylacinus + :-----1 Thylacinus branch length S.E. branch length S.E. -Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 -Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 -Dasyurus 3 0.00001 0.00200 -Echymipera 4 0.27841 0.11691 -Trichosuru 5 0.17822 0.10160 -Phalanger 6 0.27519 0.12613 -Philander 7 0.22533 0.10269 10 iterations until convergence -Bos 8 0.38507 0.14566 log L: -570.33 +Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889 +Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510 +Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178 +Echymipera 4 0.20360 0.08378 +Trichosuru 5 0.15345 0.07805 +Phalanger 6 0.18858 0.08736 +Philander 7 0.16082 0.07443 10 iterations until convergence +Bos 8 0.30632 0.12025 log L: -569.50 WARNING --- at least one branch length is close to an internal boundary! @@ -312,9 +337,9 @@ WARNING --- at least one branch length i Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, -(Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, -Philander:0.22533,Bos:0.38507); +(Thylacinus:0.13266,(Trichosuru:0.15345,Phalanger:0.18858)98:0.14146, +((Sarcophilu:0.16398,Dasyurus:0.00001)97:0.15536,Echymipera:0.20360, +Philander:0.16082,Bos:0.30632)59:0.07879); TIME STAMP --- a/tests/check-qp-jtt-prot +++ b/tests/check-qp-jtt-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -103,11 +130,11 @@ substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17343 0.93732 0.96340 2.06393 1.74159 2.60857 HBB_HORSE 0.17343 0.00000 0.97297 0.97742 2.03298 1.75271 2.65715 -HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.26 2.51688 -HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47 +HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.25126 2.51688 +HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47562 MYG_PHYCA 2.06393 2.03298 1.93956 1.99570 0.00000 2.04426 2.69086 -GLB5_PETMA 1.74159 1.75271 1.26 1.34817 2.04426 0.00000 2.23399 -LGB2_LUPLU 2.60857 2.65715 2.51688 2.47 2.69086 2.23399 0.00000 +GLB5_PETMA 1.74159 1.75271 1.25126 1.34817 2.04426 0.00000 2.23399 +LGB2_LUPLU 2.60857 2.65715 2.51688 2.47562 2.69086 2.23399 0.00000 Average distance (over all possible pairs of sequences): 1.69047 minimum : 0.12200, maximum : 2.69086 @@ -122,17 +149,17 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 6 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- - #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 + #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -174,15 +201,15 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---MYG_PHYCA - : - :100:---GLB5_PETMA - : : - :100: :---LGB2_LUPLU - : : - : : :---HBA_HUMAN - : :100: - : :---HBA_HORSE + :---HBA_HUMAN + :100: + : :---HBA_HORSE + :100: + : : :---MYG_PHYCA + : : : + : :100:---GLB5_PETMA + : : + : :---LGB2_LUPLU : :-----------HBB_HORSE : @@ -191,8 +218,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, -HBA_HORSE)100)100,HBB_HORSE); +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, +HBB_HORSE); BIPARTITIONS @@ -200,23 +227,23 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****... : 1000 - **..... : 1000 - **..*** : 1000 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 393 + *****.. : 480 (0.480) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 380 - ****..* : 227 + ****.*. : 447 (0.447) + ****..* : 73 (0.073) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -225,15 +252,15 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :--------------5 MYG_PHYCA - :------8 - : :-------6 GLB5_PETMA - : : - : :------------------7 LGB2_LUPLU + :-3 HBA_HUMAN + :----8 + : :-4 HBA_HORSE :-------10 - : : :-3 HBA_HUMAN - : :----9 - : :-4 HBA_HORSE + : : :--------------5 MYG_PHYCA + : :------9 + : :-------6 GLB5_PETMA + : : + : :------------------7 LGB2_LUPLU : :--2 HBB_HORSE : @@ -241,21 +268,21 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04638 0.03177 8 0.42254 0.12722 -HBB_HORSE 2 0.12734 0.03889 9 0.25371 0.08 +HBB_HUMAN 1 0.04638 0.03177 8 0.25373 0.08572 +HBB_HORSE 2 0.12734 0.03889 9 0.42250 0.12721 HBA_HUMAN 3 0.02556 0.02189 10 0.61836 0.11268 -HBA_HORSE 4 0.09595 0.03156 -MYG_PHYCA 5 1.31230 0.21006 -GLB5_PETMA 6 0.68479 0.13678 12 iterations until convergence -LGB2_LUPLU 7 1.72936 0.26616 log L: -1707.74 +HBA_HORSE 4 0.09596 0.03156 +MYG_PHYCA 5 1.31229 0.21005 +GLB5_PETMA 6 0.68477 0.13677 12 iterations until convergence +LGB2_LUPLU 7 1.72937 0.26616 log L: -1707.74 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04638,((MYG_PHYCA:1.31230,GLB5_PETMA:0.68479,LGB2_LUPLU:1.72936) -100:0.42254,(HBA_HUMAN:0.02556,HBA_HORSE:0.09595)100:0.25371)100:0.61836, -HBB_HORSE:0.12734); +(HBB_HUMAN:0.04638,((HBA_HUMAN:0.02556,HBA_HORSE:0.09596)100:0.25373, +(MYG_PHYCA:1.31229,GLB5_PETMA:0.68477,LGB2_LUPLU:1.72937)100:0.42250) +100:0.61836,HBB_HORSE:0.12734); TIME STAMP --- a/tests/check-qp-jtt-rhet-clock-prot +++ b/tests/check-qp-jtt-rhet-clock-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -101,64 +128,60 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 -HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 -HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 -HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 -MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 -GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 -LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 - -Average distance (over all possible pairs of sequences): 2.07265 - minimum : 0.12538, maximum : 3.42222 - variance : 1.03523, std.dev. : 1.01746 +HBB_HUMAN 0.00000 0.17871 1.04599 1.08300 2.51519 2.11125 3.24687 +HBB_HORSE 0.17871 0.00000 1.09480 1.10580 2.48701 2.13026 3.32934 +HBA_HUMAN 1.04599 1.09480 0.00000 0.12529 2.35552 1.45323 3.25521 +HBA_HORSE 1.08300 1.10580 0.12529 0.00000 2.43439 1.57394 3.14696 +MYG_PHYCA 2.51519 2.48701 2.35552 2.43439 0.00000 2.53740 3.41680 +GLB5_PETMA 2.11125 2.13026 1.45323 1.57394 2.53740 0.00000 2.84462 +LGB2_LUPLU 3.24687 3.32934 3.25521 3.14696 3.41680 2.84462 0.00000 + +Average distance (over all possible pairs of sequences): 2.07008 + minimum : 0.12529, maximum : 3.41680 + variance : 1.03242, std.dev. : 1.01608 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates -Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) -Number of Gamma rate categories: 8 +Gamma distribution parameter alpha (estimated from data set): 2.47 (S.E. 0.87) +Number of Gamma rate categories: 4 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.2882 0.1250 - 2 0.4879 0.1250 - 3 0.6513 0.1250 - 4 0.8135 0.1250 - 5 0.9910 0.1250 - 6 1.2042 0.1250 - 7 1.4978 0.1250 - 8 2.0662 0.1250 + 1 0.3690 0.2500 + 2 0.7199 0.2500 + 3 1.1100 0.2500 + 4 1.8010 0.2500 -Categories 1-8 approximate a continous Gamma-distribution with expectation 1 -and variance 0.35. +Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 +and variance 0.40. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): - 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 - 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 - 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 - 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 - 6 6 7 2 6 4 3 1 + 4 1 1 4 2 1 3 2 4 1 4 1 2 1 4 2 1 4 4 4 3 3 1 4 2 2 1 2 1 3 + 1 4 3 4 1 4 1 2 2 4 1 4 4 1 2 1 1 3 3 1 2 2 1 1 4 1 1 4 2 1 + 4 4 1 3 4 4 2 2 4 2 4 2 4 3 4 4 3 1 2 4 1 1 4 4 1 1 4 1 4 3 + 1 1 4 1 1 3 2 2 3 3 2 1 3 4 1 2 2 4 3 2 1 3 4 3 1 4 3 3 4 2 + 3 3 4 1 3 2 2 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 6 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- - #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 + #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -200,15 +223,15 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---MYG_PHYCA - : - :100:---GLB5_PETMA - : : - :100: :---LGB2_LUPLU - : : - : : :---HBA_HUMAN - : :100: - : :---HBA_HORSE + :---HBA_HUMAN + :100: + : :---HBA_HORSE + :100: + : : :---MYG_PHYCA + : : : + : :100:---GLB5_PETMA + : : + : :---LGB2_LUPLU : :-----------HBB_HORSE : @@ -217,8 +240,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, -HBA_HORSE)100)100,HBB_HORSE); +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, +HBB_HORSE); BIPARTITIONS @@ -226,23 +249,23 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****... : 1000 - **..... : 1000 - **..*** : 1000 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 393 + *****.. : 480 (0.480) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 380 - ****..* : 227 + ****.*. : 447 (0.447) + ****..* : 73 (0.073) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -251,15 +274,15 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :--------------5 MYG_PHYCA - :-----8 - : :-------6 GLB5_PETMA - : : - : :-------------------7 LGB2_LUPLU + :-3 HBA_HUMAN + :---8 + : :-4 HBA_HORSE :------10 - : : :-3 HBA_HUMAN - : :---9 - : :-4 HBA_HORSE + : : :--------------5 MYG_PHYCA + : :-----9 + : :-------6 GLB5_PETMA + : : + : :-------------------7 LGB2_LUPLU : :--2 HBB_HORSE : @@ -267,21 +290,21 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 -HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 -HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 -HBA_HORSE 4 0.10548 0.03367 -MYG_PHYCA 5 1.68057 0.30228 -GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence -LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 +HBB_HUMAN 1 0.04960 0.03397 8 0.23079 0.10535 +HBB_HORSE 2 0.12883 0.04077 9 0.50896 0.17274 +HBA_HUMAN 3 0.01975 0.02294 10 0.74671 0.14184 +HBA_HORSE 4 0.10545 0.03361 +MYG_PHYCA 5 1.67907 0.30134 +GLB5_PETMA 6 0.80699 0.18542 11 iterations until convergence +LGB2_LUPLU 7 2.33192 0.42328 log L: -1701.58 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) -100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, -HBB_HORSE:0.12953); +(HBB_HUMAN:0.04960,((HBA_HUMAN:0.01975,HBA_HORSE:0.10545)100:0.23079, +(MYG_PHYCA:1.67907,GLB5_PETMA:0.80699,LGB2_LUPLU:2.33192)100:0.50896) +100:0.74671,HBB_HORSE:0.12883); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -295,15 +318,15 @@ If the automatic search misplaces the ro (rename "outtree" to "intree") and select location of root manually! - :----------5 MYG_PHYCA + :-3 HBA_HUMAN :------8 - : :----------6 GLB5_PETMA - : : - : :------------------7 LGB2_LUPLU + : :-4 HBA_HORSE :----10 - : : :-3 HBA_HUMAN + : : :----------5 MYG_PHYCA : :------9 - : :-4 HBA_HORSE + : :----------6 GLB5_PETMA + : : + : :------------------7 LGB2_LUPLU : :-2 HBB_HORSE : @@ -313,38 +336,38 @@ If the automatic search misplaces the ro Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) -HBB_HUMAN 1 0.08775 0. 8 0.58020 0.874 -HBB_HORSE 2 0.08775 1.476 9 0.51495 0.454 -HBA_HUMAN 3 0.06493 0.307 10 0.49213 1.519 -HBA_HORSE 4 0.06493 1.625 -MYG_PHYCA 5 1.16008 1.449 -GLB5_PETMA 6 1.16008 0.700 7 iterations until convergence -LGB2_LUPLU 7 2.28806 1.020 log L: -1708.27 +HBB_HUMAN 1 0.08750 0.567 8 0.51287 0.450 +HBB_HORSE 2 0.08750 1.472 9 0.57972 0.878 +HBA_HUMAN 3 0.06482 0.305 10 0.49019 1.523 +HBA_HORSE 4 0.06482 1.627 +MYG_PHYCA 5 1.15741 1.451 +GLB5_PETMA 6 1.15741 0.697 7 iterations until convergence +LGB2_LUPLU 7 2.28390 1.021 log L: -1708.22 height S.E. of node common to branches -0.06493 0.01761 9 3 4 -0.08775 0.02041 10 2 1 -0.57988 0.07414 8 9 10 -1.16008 0.11361 7 8 5 6 -1.72407 0.21630 of root at branch 7 +0.08750 0.02034 10 2 1 +0.06482 0.01758 8 3 4 +0.57769 0.07382 9 10 8 +1.15741 0.11326 7 9 5 6 +1.72066 0.21547 of root at branch 7 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(LGB2_LUPLU:1.72407,(((HBA_HUMAN:0.06493,HBA_HORSE:0.06493)100:0.51495 -,(HBB_HORSE:0.08775,HBB_HUMAN:0.08775):0.49213):0.58020,MYG_PHYCA:1.16008, -GLB5_PETMA:1.16008):0.56399); +(LGB2_LUPLU:1.72066,(((HBB_HORSE:0.08750,HBB_HUMAN:0.08750):0.49019 +,(HBA_HUMAN:0.06482,HBA_HORSE:0.06482)100:0.51287):0.57972,MYG_PHYCA:1.15741, +GLB5_PETMA:1.15741):0.56324); MOLECULAR CLOCK LIKELIHOOD RATIO TEST -log L without clock: -1701.69 (independent branch parameters: 10) -log L with clock: -1708.27 (independent branch parameters: 5) +log L without clock: -1701.58 (independent branch parameters: 10) +log L with clock: -1708.22 (independent branch parameters: 5) -Likelihood ratio test statistic delta: 13.15 +Likelihood ratio test statistic delta: 13.28 Degress of freedom of chi-square distribution: 5 -Critical significance level: 2.20% +Critical significance level: 2.09% The simpler (clocklike) tree is rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree is --- a/tests/check-qp-jtt-rhet-prot +++ b/tests/check-qp-jtt-rhet-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -101,64 +128,60 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 -HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 -HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 -HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 -MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 -GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 -LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 - -Average distance (over all possible pairs of sequences): 2.07265 - minimum : 0.12538, maximum : 3.42222 - variance : 1.03523, std.dev. : 1.01746 +HBB_HUMAN 0.00000 0.17871 1.04599 1.08300 2.51519 2.11125 3.24687 +HBB_HORSE 0.17871 0.00000 1.09480 1.10580 2.48701 2.13026 3.32934 +HBA_HUMAN 1.04599 1.09480 0.00000 0.12529 2.35552 1.45323 3.25521 +HBA_HORSE 1.08300 1.10580 0.12529 0.00000 2.43439 1.57394 3.14696 +MYG_PHYCA 2.51519 2.48701 2.35552 2.43439 0.00000 2.53740 3.41680 +GLB5_PETMA 2.11125 2.13026 1.45323 1.57394 2.53740 0.00000 2.84462 +LGB2_LUPLU 3.24687 3.32934 3.25521 3.14696 3.41680 2.84462 0.00000 + +Average distance (over all possible pairs of sequences): 2.07008 + minimum : 0.12529, maximum : 3.41680 + variance : 1.03242, std.dev. : 1.01608 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates -Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) -Number of Gamma rate categories: 8 +Gamma distribution parameter alpha (estimated from data set): 2.47 (S.E. 0.87) +Number of Gamma rate categories: 4 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.2882 0.1250 - 2 0.4879 0.1250 - 3 0.6513 0.1250 - 4 0.8135 0.1250 - 5 0.9910 0.1250 - 6 1.2042 0.1250 - 7 1.4978 0.1250 - 8 2.0662 0.1250 + 1 0.3690 0.2500 + 2 0.7199 0.2500 + 3 1.1100 0.2500 + 4 1.8010 0.2500 -Categories 1-8 approximate a continous Gamma-distribution with expectation 1 -and variance 0.35. +Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 +and variance 0.40. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): - 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 - 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 - 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 - 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 - 6 6 7 2 6 4 3 1 + 4 1 1 4 2 1 3 2 4 1 4 1 2 1 4 2 1 4 4 4 3 3 1 4 2 2 1 2 1 3 + 1 4 3 4 1 4 1 2 2 4 1 4 4 1 2 1 1 3 3 1 2 2 1 1 4 1 1 4 2 1 + 4 4 1 3 4 4 2 2 4 2 4 2 4 3 4 4 3 1 2 4 1 1 4 4 1 1 4 1 4 3 + 1 1 4 1 1 3 2 2 3 3 2 1 3 4 1 2 2 4 3 2 1 3 4 3 1 4 3 3 4 2 + 3 3 4 1 3 2 2 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 6 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- - #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 + #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -200,15 +223,15 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---MYG_PHYCA - : - :100:---GLB5_PETMA - : : - :100: :---LGB2_LUPLU - : : - : : :---HBA_HUMAN - : :100: - : :---HBA_HORSE + :---HBA_HUMAN + :100: + : :---HBA_HORSE + :100: + : : :---MYG_PHYCA + : : : + : :100:---GLB5_PETMA + : : + : :---LGB2_LUPLU : :-----------HBB_HORSE : @@ -217,8 +240,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, -HBA_HORSE)100)100,HBB_HORSE); +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, +HBB_HORSE); BIPARTITIONS @@ -226,23 +249,23 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****... : 1000 - **..... : 1000 - **..*** : 1000 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 393 + *****.. : 480 (0.480) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 380 - ****..* : 227 + ****.*. : 447 (0.447) + ****..* : 73 (0.073) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -251,15 +274,15 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :--------------5 MYG_PHYCA - :-----8 - : :-------6 GLB5_PETMA - : : - : :-------------------7 LGB2_LUPLU + :-3 HBA_HUMAN + :---8 + : :-4 HBA_HORSE :------10 - : : :-3 HBA_HUMAN - : :---9 - : :-4 HBA_HORSE + : : :--------------5 MYG_PHYCA + : :-----9 + : :-------6 GLB5_PETMA + : : + : :-------------------7 LGB2_LUPLU : :--2 HBB_HORSE : @@ -267,21 +290,21 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 -HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 -HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 -HBA_HORSE 4 0.10548 0.03367 -MYG_PHYCA 5 1.68057 0.30228 -GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence -LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 +HBB_HUMAN 1 0.04960 0.03397 8 0.23079 0.10535 +HBB_HORSE 2 0.12883 0.04077 9 0.50896 0.17274 +HBA_HUMAN 3 0.01975 0.02294 10 0.74671 0.14184 +HBA_HORSE 4 0.10545 0.03361 +MYG_PHYCA 5 1.67907 0.30134 +GLB5_PETMA 6 0.80699 0.18542 11 iterations until convergence +LGB2_LUPLU 7 2.33192 0.42328 log L: -1701.58 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) -100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, -HBB_HORSE:0.12953); +(HBB_HUMAN:0.04960,((HBA_HUMAN:0.01975,HBA_HORSE:0.10545)100:0.23079, +(MYG_PHYCA:1.67907,GLB5_PETMA:0.80699,LGB2_LUPLU:2.33192)100:0.50896) +100:0.74671,HBB_HORSE:0.12883); TIME STAMP --- a/tests/check-qp-mtrev-prot +++ b/tests/check-qp-mtrev-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: mtREV24 (Adachi-Hasegawa 1996) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -104,9 +131,9 @@ substitution and rate heterogeneity. HBB_HUMAN 0.00000 0.19615 1.12348 1.16856 2.59690 2.15305 3.47989 HBB_HORSE 0.19615 0.00000 1.17857 1.20524 2.74793 2.18071 3.63316 HBA_HUMAN 1.12348 1.17857 0.00000 0.13144 2.41361 1.43785 3.06000 -HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55 3.05140 +HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55582 3.05140 MYG_PHYCA 2.59690 2.74793 2.41361 2.44163 0.00000 2.62256 3.47779 -GLB5_PETMA 2.15305 2.18071 1.43785 1.55 2.62256 0.00000 2.97722 +GLB5_PETMA 2.15305 2.18071 1.43785 1.55582 2.62256 0.00000 2.97722 LGB2_LUPLU 3.47989 3.63316 3.06000 3.05140 3.47779 2.97722 0.00000 Average distance (over all possible pairs of sequences): 2.13490 @@ -122,17 +149,17 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 18 [ 90.00%] 1 [ 5.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 - HBA_HORSE 18 [ 90.00%] 2 [ 10.00%] 0 [ 0.00%] 20 - MYG_PHYCA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 - GLB5_PETMA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 2 [ 10.00%] 2 [ 10.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 18 [ 90.00%] 1 [ 5.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 + 4 HBA_HORSE 18 [ 90.00%] 2 [ 10.00%] 0 [ 0.00%] 20 + 5 MYG_PHYCA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 + 6 GLB5_PETMA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 2 [ 10.00%] 2 [ 10.00%] 20 -------------------------------------------------------------------------- - #quartets : 30 [ 85.71%] 3 [ 8.57%] 2 [ 5.71%] 35 + #quartets : 30 [ 85.71%] 3 [ 8.57%] 2 [ 5.71%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -180,7 +207,7 @@ This quartet puzzling tree is not comple :100: : : :---MYG_PHYCA : : : - : :-97:---GLB5_PETMA + : :-96:---GLB5_PETMA : : : :---LGB2_LUPLU : @@ -191,7 +218,7 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)97)100, +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)96)100, HBB_HORSE); @@ -200,26 +227,26 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - **..... : 1000 - **..*** : 1000 - ****... : 971 + **..*** : 1000 (1.000) + **..... : 1000 (1.000) + ****... : 957 (0.957) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 462 + *****.. : 492 (0.492) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 436 - ****..* : 100 - **..*.* : 15 - **..*.. : 14 - **....* : 2 + ****.*. : 476 (0.476) + ****..* : 31 (0.031) + **..*.* : 24 (0.024) + **..*.. : 19 (0.019) + **....* : 1 (0.001) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -257,7 +284,7 @@ Consensus tree with maximum likelihood b (in CLUSTAL W notation): (HBB_HUMAN:0.03472,((HBA_HUMAN:0.04636,HBA_HORSE:0.08355)100:0.30126, -(MYG_PHYCA:1.58550,GLB5_PETMA:0.88663,LGB2_LUPLU:2.13259)97:0.34149) +(MYG_PHYCA:1.58550,GLB5_PETMA:0.88663,LGB2_LUPLU:2.13259)96:0.34149) 100:0.70896,HBB_HORSE:0.16246); --- a/tests/check-qp-pure-bin +++ b/tests/check-qp-pure-bin @@ -14,10 +14,34 @@ SEQUENCE ALIGNMENT Input data: 5 sequences with 895 binary state sites Number of constant sites: 825 (= 92.2% of all sites) + Number of site patterns: 16 Number of constant site patterns: 2 (= 12.5% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 15 (= 1.7% of all sites) + - fully informative sites: 15 (= 1.7% of all sites) + - partly informative sites: 0 (= 0.0% of all sites) +Number of parsimony uninformative sites: 880 (= 98.3% of all sites) + - variable, but uninformative sites: 55 (= 6.1% of all sites) + - completely constant sites: 825 (= 92.2% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Gibbon 15 ( 1.68%) 880 ( 98.32%) + 2 Human 15 ( 1.68%) 880 ( 98.32%) + 3 Chimpanzee 15 ( 1.68%) 880 ( 98.32%) + 4 Gorilla 15 ( 1.68%) 880 ( 98.32%) + 5 Orangutan 15 ( 1.68%) 880 ( 98.32%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: Two-state model (Felsenstein 1981) @@ -29,14 +53,14 @@ Binary state frequencies (estimated from AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Gibbon 0 0 0 0.00% - Human 0 0 0 0.00% - Chimpanzee 0 0 0 0.00% - Gorilla 0 0 0 0.00% - Orangutan 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 Gibbon 0 0 0 0.00% + 2 Human 0 0 0 0.00% + 3 Chimpanzee 0 0 0 0.00% + 4 Gorilla 0 0 0 0.00% + 5 Orangutan 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -51,15 +75,16 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Gibbon passed 41.61% - Human passed 73.47% - Chimpanzee passed 68.43% - Gorilla passed 94.60% - Orangutan passed 100.00% - -The chi-square tests compares the binary state composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Gibbon passed 41.61% (0.66) + 2 Human passed 73.47% (0.11) + 3 Chimpanzee passed 68.43% (0.17) + 4 Gorilla passed 94.60% (0.00) + 5 Orangutan passed 100.00% (0.00) + +The chi-square tests with 1 degrees of freedom compares the +binary state composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -95,15 +120,15 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Gibbon 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 - Human 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 - Chimpanzee 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 - Gorilla 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 - Orangutan 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Gibbon 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 + 2 Human 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 + 3 Chimpanzee 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 + 4 Gorilla 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 + 5 Orangutan 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 -------------------------------------------------------------------------- - #quartets : 5 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 5 + #quartets : 5 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 5 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -166,14 +191,14 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..** : 1000 - *...* : 1000 + *..** : 1000 (1.000) + *...* : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) None (all bipartitions are included) --- a/tests/check-qp-pure-nucl +++ b/tests/check-qp-pure-nucl @@ -14,10 +14,37 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) @@ -45,17 +72,17 @@ Expected pyrimidine transition/purine tr AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -70,18 +97,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -98,19 +126,19 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25 0.22032 0.24509 0.26007 0.24938 0.22246 +Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 -Sarcophilu 0.25 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 +Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 -Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28 +Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 -Philander 0.22246 0.26008 0.17801 0.23041 0.28 0.29036 0.00000 +Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 @@ -128,18 +156,18 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 - Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 - Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 - Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 - Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 - Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 - Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 - Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 + 2 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 + 3 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 + 4 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 + 5 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 + 6 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 + 7 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 + 8 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- - #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 + #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -182,15 +210,15 @@ This quartet puzzling tree is not comple :---Trichosuru - :-----97: + :----100: : :---Phalanger : : :---Sarcophilu - : :-98: + : :100: : : :---Dasyurus : : - :-71: :---Philander - : :-65: + :-73: :---Philander + : :-71: : : :---Bos : : : :-------Echymipera @@ -200,8 +228,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, -(Philander,Bos)65,Echymipera)71); +(Thylacinus,(Trichosuru,Phalanger)100,((Sarcophilu,Dasyurus)100, +(Philander,Bos)71,Echymipera)73); BIPARTITIONS @@ -209,44 +237,44 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 981 - ****..** : 971 - *...**.. : 713 - ******.. : 649 + ****..** : 999 (0.999) + *..***** : 999 (0.999) + *...**.. : 730 (0.730) + ******.. : 711 (0.711) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 426 + *...**** : 466 (0.466) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 347 - ***.**.* : 150 - *...**.* : 131 - *..***.. : 87 - *..*..** : 81 - *.....** : 72 - ****..*. : 55 - ***.***. : 37 - ****.... : 36 - *..***.* : 36 - ***..... : 31 - *.....*. : 28 - *...***. : 27 - *......* : 27 - *....*.. : 26 - *..*.... : 21 - **..**** : 16 - ***...** : 14 - *..*..*. : 13 - *..****. : 12 + ***.**.. : 333 (0.333) + *...**.* : 171 (0.171) + ***.**.* : 89 (0.089) + *..***.. : 80 (0.080) + *.....** : 79 (0.079) + *..*..** : 69 (0.069) + ****..*. : 51 (0.051) + *......* : 34 (0.034) + *..***.* : 30 (0.030) + ****.... : 28 (0.028) + ***.***. : 27 (0.027) + *..*.... : 22 (0.022) + *...***. : 20 (0.020) + ***..... : 19 (0.019) + *.....*. : 14 (0.014) + *..****. : 9 (0.009) + *..*..*. : 8 (0.008) + ***...** : 6 (0.006) + ***....* : 4 (0.004) + ****.**. : 1 (0.001) -(6 other less frequent bipartitions not shown) +(1 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -275,7 +303,7 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 -Dasyurus 3 0.00 0.01273 11 0.04220 0.02513 +Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 @@ -286,9 +314,9 @@ Bos 8 0.13479 0.04095 lo Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, -((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995, -Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); +(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953, +((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995, +Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457); TIME STAMP --- a/tests/check-qp-pure-prot +++ b/tests/check-qp-pure-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -122,17 +149,17 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 20 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 20 - HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 - GLB5_PETMA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 - LGB2_LUPLU 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 20 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 + 6 GLB5_PETMA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 + 7 LGB2_LUPLU 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- - #quartets : 32 [ 91.43%] 0 [ 0.00%] 3 [ 8.57%] 35 + #quartets : 32 [ 91.43%] 0 [ 0.00%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -179,7 +206,7 @@ This quartet puzzling tree is completely : :---HBA_HORSE :100: : : :---GLB5_PETMA - : : :-54: + : : :-82: : :100: :---LGB2_LUPLU : : : :-------MYG_PHYCA @@ -191,7 +218,7 @@ This quartet puzzling tree is completely Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,((GLB5_PETMA,LGB2_LUPLU)54, +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,((GLB5_PETMA,LGB2_LUPLU)82, MYG_PHYCA)100)100,HBB_HORSE); @@ -200,24 +227,24 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - **..... : 1000 - **..*** : 1000 - ****... : 1000 - *****.. : 544 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) + *****.. : 821 (0.821) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) None (No congruent split not included) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 234 - ****..* : 222 + ****..* : 105 (0.105) + ****.*. : 74 (0.074) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -244,8 +271,8 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. HBB_HUMAN 1 0.04915 0.03158 8 0.28345 0.08777 HBB_HORSE 2 0.12603 0.03871 9 0.18154 0.13086 -HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12 -HBA_HORSE 4 0.09 0.03153 11 0.60239 0.11261 +HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12552 +HBA_HORSE 4 0.09542 0.03153 11 0.60239 0.11261 MYG_PHYCA 5 1.33166 0.21117 GLB5_PETMA 6 0.57466 0.13843 10 iterations until convergence LGB2_LUPLU 7 1.71333 0.27645 log L: -1699.00 @@ -254,8 +281,8 @@ LGB2_LUPLU 7 1.71333 0.27645 lo Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09)100:0.28345, -((GLB5_PETMA:0.57466,LGB2_LUPLU:1.71333)54:0.18154,MYG_PHYCA:1.33166) +(HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345, +((GLB5_PETMA:0.57466,LGB2_LUPLU:1.71333)82:0.18154,MYG_PHYCA:1.33166) 100:0.34694)100:0.60239,HBB_HORSE:0.12603); --- a/tests/check-qp-tn-nucl +++ b/tests/check-qp-tn-nucl @@ -14,23 +14,50 @@ SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) + Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 31 (= 26.7% of all sites) + - fully informative sites: 23 (= 19.8% of all sites) + - partly informative sites: 8 (= 6.9% of all sites) +Number of parsimony uninformative sites: 85 (= 73.3% of all sites) + - variable, but uninformative sites: 19 (= 16.4% of all sites) + - completely constant sites: 66 (= 56.9% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 Thylacinus 30 ( 25.86%) 86 ( 74.14%) + 2 Sarcophilu 29 ( 25.00%) 87 ( 75.00%) + 3 Dasyurus 30 ( 25.86%) 86 ( 74.14%) + 4 Echymipera 29 ( 25.00%) 87 ( 75.00%) + 5 Trichosuru 29 ( 25.00%) 87 ( 75.00%) + 6 Phalanger 30 ( 25.86%) 86 ( 74.14%) + 7 Philander 31 ( 26.72%) 85 ( 73.28%) + 8 Bos 29 ( 25.00%) 87 ( 75.00%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: TN (Tamura-Nei 1993) -Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.61) -Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.65) +Transition/transversion parameter (estimated from data set): 1.25 (S.E. 0.40) +Y/R transition parameter (estimated from data set): 2.26 (S.E. 0.89) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 - A-G rate: 1.52641 + A-G rate: 1.54307 A-T rate: 1.00000 C-G rate: 1.00000 - C-T rate: 3.42338 + C-T rate: 3.45671 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): @@ -40,23 +67,23 @@ Nucleotide frequencies (estimated from d pi(G) = 12.0% pi(T) = 30.7% -Expected transition/transversion ratio: 1.57 -Expected pyrimidine transition/purine transition ratio: 6.69 +Expected transition/transversion ratio: 1.58 +Expected pyrimidine transition/purine transition ratio: 6.68 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - Thylacinus 0 0 0 0.00% - Sarcophilu 0 0 0 0.00% - Dasyurus 0 1 1 0.86% - Echymipera 0 0 0 0.00% - Trichosuru 0 0 0 0.00% - Phalanger 0 0 0 0.00% - Philander 0 0 0 0.00% - Bos 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 1 1 0.11% + gaps wildcards sum % sequence + 1 Thylacinus 0 0 0 0.00% + 2 Sarcophilu 0 0 0 0.00% + 3 Dasyurus 0 1 1 0.86% + 4 Echymipera 0 0 0 0.00% + 5 Trichosuru 0 0 0 0.00% + 6 Phalanger 0 0 0 0.00% + 7 Philander 0 0 0 0.00% + 8 Bos 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,18 +98,19 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - Thylacinus passed 90.89% - Sarcophilu passed 93.32% - Dasyurus passed 98.01% - Echymipera passed 92.83% - Trichosuru passed 90.41% - Phalanger passed 86.09% - Philander passed 66.19% - Bos passed 60.02% - -The chi-square tests compares the nucleotide composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 Thylacinus passed 90.89% (0.54) + 2 Sarcophilu passed 93.32% (0.43) + 3 Dasyurus passed 98.01% (0.18) + 4 Echymipera passed 92.83% (0.46) + 5 Trichosuru passed 90.41% (0.57) + 6 Phalanger passed 86.09% (0.75) + 7 Philander passed 66.19% (1.59) + 8 Bos passed 60.02% (1.87) + +The chi-square tests with 3 degrees of freedom compares the +nucleotide composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES @@ -99,26 +127,26 @@ Maximum likelihood distances are compute substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25968 0.22378 0.26 0.26619 0.25302 0.22610 - 0.24162 -Sarcophilu 0.25968 0.00000 0.13240 0.27376 0.28965 0.33121 0.26282 - 0.30169 -Dasyurus 0.22378 0.13240 0.00000 0.20328 0.25274 0.25432 0.17972 - 0.24235 -Echymipera 0.26 0.27376 0.20328 0.00000 0.30289 0.34430 0.23479 - 0.27773 -Trichosuru 0.26619 0.28965 0.25274 0.30289 0.00000 0.21414 0.29157 - 0.27782 -Phalanger 0.25302 0.33121 0.25432 0.34430 0.21414 0.00000 0.29425 - 0.33 -Philander 0.22610 0.26282 0.17972 0.23479 0.29157 0.29425 0.00000 - 0.22749 -Bos 0.24162 0.30169 0.24235 0.27773 0.27782 0.33 0.22749 +Thylacinus 0.00000 0.25985 0.22390 0.25044 0.26641 0.25322 0.22626 + 0.24180 +Sarcophilu 0.25985 0.00000 0.13242 0.27396 0.28989 0.33153 0.26303 + 0.30195 +Dasyurus 0.22390 0.13242 0.00000 0.20339 0.25292 0.25452 0.17982 + 0.24252 +Echymipera 0.25044 0.27396 0.20339 0.00000 0.30315 0.34463 0.23492 + 0.27794 +Trichosuru 0.26641 0.28989 0.25292 0.30315 0.00000 0.21427 0.29184 + 0.27804 +Phalanger 0.25322 0.33153 0.25452 0.34463 0.21427 0.00000 0.29454 + 0.33617 +Philander 0.22626 0.26303 0.17982 0.23492 0.29184 0.29454 0.00000 + 0.22765 +Bos 0.24180 0.30195 0.24252 0.27794 0.27804 0.33617 0.22765 0.00000 -Average distance (over all possible pairs of sequences): 0.25876 - minimum : 0.13240, maximum : 0.34430 - variance : 0.00217, std.dev. : 0.04653 +Average distance (over all possible pairs of sequences): 0.25896 + minimum : 0.13242, maximum : 0.34463 + variance : 0.00217, std.dev. : 0.04660 RATE HETEROGENEITY @@ -129,18 +157,18 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - Thylacinus 21 [ 60.00%] 4 [ 11.43%] 10 [ 28.57%] 35 - Sarcophilu 26 [ 74.29%] 1 [ 2.86%] 8 [ 22.86%] 35 - Dasyurus 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 - Echymipera 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 - Trichosuru 25 [ 71.43%] 4 [ 11.43%] 6 [ 17.14%] 35 - Phalanger 28 [ 80.00%] 1 [ 2.86%] 6 [ 17.14%] 35 - Philander 23 [ 65.71%] 5 [ 14.29%] 7 [ 20.00%] 35 - Bos 19 [ 54.29%] 4 [ 11.43%] 12 [ 34.29%] 35 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 Thylacinus 21 [ 60.00%] 4 [ 11.43%] 10 [ 28.57%] 35 + 2 Sarcophilu 26 [ 74.29%] 1 [ 2.86%] 8 [ 22.86%] 35 + 3 Dasyurus 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 + 4 Echymipera 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 + 5 Trichosuru 25 [ 71.43%] 4 [ 11.43%] 6 [ 17.14%] 35 + 6 Phalanger 28 [ 80.00%] 1 [ 2.86%] 6 [ 17.14%] 35 + 7 Philander 23 [ 65.71%] 5 [ 14.29%] 7 [ 20.00%] 35 + 8 Bos 19 [ 54.29%] 4 [ 11.43%] 12 [ 34.29%] 35 -------------------------------------------------------------------------- - #quartets : 47 [ 67.14%] 6 [ 8.57%] 17 [ 24.29%] 70 + #quartets : 47 [ 67.14%] 6 [ 8.57%] 17 [ 24.29%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -179,30 +207,30 @@ QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. -This quartet puzzling tree is not completely resolved! +This quartet puzzling tree is completely resolved. - :---Trichosuru - :-----94: - : :---Phalanger - : - : :---Sarcophilu - : :-98: - : : :---Dasyurus - : : - :-63: :---Philander - : :-67: - : : :---Bos - : : - : :-------Echymipera - : - :-----------Thylacinus + :---Trichosuru + :--------100: + : :---Phalanger + : + : :---Philander + : :-----69: + : : :---Bos + :-70: + : : :---Sarcophilu + : : :100: + : :-53: :---Dasyurus + : : + : :-------Echymipera + : + :---------------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): -(Thylacinus,(Trichosuru,Phalanger)94,((Sarcophilu,Dasyurus)98, -(Philander,Bos)67,Echymipera)63); +(Thylacinus,(Trichosuru,Phalanger)100,((Philander,Bos)69,(( +Sarcophilu,Dasyurus)100,Echymipera)53)70); BIPARTITIONS @@ -210,44 +238,45 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *..***** : 979 - ****..** : 935 - ******.. : 666 - *...**.. : 629 + ****..** : 1000 (1.000) + *..***** : 1000 (1.000) + *...**.. : 704 (0.704) + ******.. : 692 (0.692) + *...**** : 528 (0.528) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 422 + None (No congruent split not included) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 271 - *..***.. : 132 - *...**.* : 122 - ***.**.* : 112 - *..*..** : 94 - *.....** : 88 - ****.... : 83 - ****..*. : 79 - *..*.... : 65 - *....*.. : 56 - *..***.* : 49 - ***.***. : 40 - ***..... : 36 - **..**** : 21 - *..*..*. : 21 - *.....*. : 20 - *......* : 19 - *...***. : 17 - ***...** : 13 - ****.**. : 7 + ***.**.. : 191 (0.191) + *...**.* : 183 (0.183) + *..***.. : 128 (0.128) + ****..*. : 81 (0.081) + *.....** : 79 (0.079) + ***.**.* : 76 (0.076) + *..*..** : 68 (0.068) + ****.... : 58 (0.058) + *..*.... : 41 (0.041) + *......* : 39 (0.039) + *..***.* : 37 (0.037) + *...***. : 17 (0.017) + *.....*. : 16 (0.016) + ***..... : 14 (0.014) + ***.***. : 12 (0.012) + ***...** : 11 (0.011) + *..*..*. : 9 (0.009) + *..****. : 7 (0.007) + ***...*. : 4 (0.004) + *..*...* : 3 (0.003) -(9 other less frequent bipartitions not shown) +(2 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -260,36 +289,36 @@ substitution and rate heterogeneity. :------9 : :----------6 Phalanger : - : :----------2 Sarcophilu - : :-------10 - : : :-3 Dasyurus - :-----12 - : : :-------7 Philander - : :----11 - : : :-----------8 Bos - : : - : :------------4 Echymipera + : :-------7 Philander + : :----10 + : : :-----------8 Bos + :----13 + : : :----------2 Sarcophilu + : : :------11 + : : : :-3 Dasyurus + : :---12 + : :-----------4 Echymipera : :---------1 Thylacinus branch length S.E. branch length S.E. -Thylacinus 1 0.11472 0.03957 9 0.04 0.03453 -Sarcophilu 2 0.12889 0.03726 10 0.08141 0.03441 -Dasyurus 3 0.00946 0.01286 11 0.04411 0.02610 -Echymipera 4 0.14312 0.04216 12 0.09 0.03071 -Trichosuru 5 0.10849 0.03850 -Phalanger 6 0.12332 0.04128 -Philander 7 0.09008 0.03478 7 iterations until convergence -Bos 8 0.13724 0.04194 log L: -600.80 +Thylacinus 1 0.11294 0.03951 9 0.06396 0.03574 +Sarcophilu 2 0.12830 0.03720 10 0.03927 0.02464 +Dasyurus 3 0.01046 0.01329 11 0.06846 0.03213 +Echymipera 4 0.13275 0.04059 12 0.02637 0.02260 +Trichosuru 5 0.10847 0.03861 13 0.04080 0.02830 +Phalanger 6 0.12347 0.04146 +Philander 7 0.08552 0.03431 8 iterations until convergence +Bos 8 0.13891 0.04250 log L: -599.59 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.04, -((Sarcophilu:0.12889,Dasyurus:0.00946)98:0.08141,(Philander:0.09008, -Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.09); +(Thylacinus:0.11294,(Trichosuru:0.10847,Phalanger:0.12347)100:0.06396, +((Philander:0.08552,Bos:0.13891)69:0.03927,((Sarcophilu:0.12830, +Dasyurus:0.01046)100:0.06846,Echymipera:0.13275)53:0.02637)70:0.04080); TIME STAMP --- a/tests/check-qp-vt-prot +++ b/tests/check-qp-vt-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: VT (Mueller-Vingron 2000) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -122,17 +149,17 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 - GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + 6 GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 -------------------------------------------------------------------------- - #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 + #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -174,15 +201,15 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---MYG_PHYCA - : - :100:---GLB5_PETMA - : : - :100: :---LGB2_LUPLU - : : - : : :---HBA_HUMAN - : :100: - : :---HBA_HORSE + :---HBA_HUMAN + :100: + : :---HBA_HORSE + :100: + : : :---MYG_PHYCA + : : : + : :100:---GLB5_PETMA + : : + : :---LGB2_LUPLU : :-----------HBB_HORSE : @@ -191,8 +218,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, -HBA_HORSE)100)100,HBB_HORSE); +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, +HBB_HORSE); BIPARTITIONS @@ -200,23 +227,23 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****... : 1000 - **..... : 1000 - **..*** : 1000 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 347 + ****.*. : 347 (0.347) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****..* : 331 - ****.*. : 322 + *****.. : 341 (0.341) + ****..* : 312 (0.312) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -225,15 +252,15 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :-------------5 MYG_PHYCA - :-------8 - : :--------6 GLB5_PETMA - : : - : :------------------7 LGB2_LUPLU + :-3 HBA_HUMAN + :-----8 + : :--4 HBA_HORSE :-------10 - : : :-3 HBA_HUMAN - : :-----9 - : :--4 HBA_HORSE + : : :-------------5 MYG_PHYCA + : :-------9 + : :--------6 GLB5_PETMA + : : + : :------------------7 LGB2_LUPLU : :--2 HBB_HORSE : @@ -241,21 +268,21 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04599 0.03062 8 0.42025 0.11481 -HBB_HORSE 2 0.12231 0.03740 9 0.25241 0.08069 -HBA_HUMAN 3 0.03150 0.02213 10 0.96 0.10035 +HBB_HUMAN 1 0.04599 0.03062 8 0.25241 0.08069 +HBB_HORSE 2 0.12231 0.03740 9 0.42027 0.11482 +HBA_HUMAN 3 0.03150 0.02213 10 0.54295 0.10035 HBA_HORSE 4 0.08803 0.03011 -MYG_PHYCA 5 1.02811 0.16334 -GLB5_PETMA 6 0.60661 0.11823 12 iterations until convergence -LGB2_LUPLU 7 1.38558 0.20879 log L: -1703.59 +MYG_PHYCA 5 1.02820 0.16336 +GLB5_PETMA 6 0.60660 0.11823 11 iterations until convergence +LGB2_LUPLU 7 1.38557 0.20879 log L: -1703.59 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04599,((MYG_PHYCA:1.02811,GLB5_PETMA:0.60661,LGB2_LUPLU:1.38558) -100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.96, -HBB_HORSE:0.12231); +(HBB_HUMAN:0.04599,((HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241, +(MYG_PHYCA:1.02820,GLB5_PETMA:0.60660,LGB2_LUPLU:1.38557)100:0.42027) +100:0.54295,HBB_HORSE:0.12231); TIME STAMP --- a/tests/check-qp-wag-prot +++ b/tests/check-qp-wag-prot @@ -14,10 +14,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: WAG (Whelan-Goldman 2000) @@ -47,16 +73,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -71,20 +97,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -122,17 +149,17 @@ Model of rate heterogeneity: uniform rat QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) - name | resolved | partly resolved | unresolved | sum - -------------------------------------------------------------------------- - HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 - MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 - GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 - LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + name | resolved | partly resolved | unresolved | sum + ------------------------------------------------------------------------------ + 1 HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 2 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 3 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 4 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 + 5 MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + 6 GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 + 7 LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 -------------------------------------------------------------------------- - #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 + #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage @@ -174,15 +201,15 @@ tree topology is shown in percent. This quartet puzzling tree is not completely resolved! - :---MYG_PHYCA - : - :100:---GLB5_PETMA - : : - :100: :---LGB2_LUPLU - : : - : : :---HBA_HUMAN - : :100: - : :---HBA_HORSE + :---HBA_HUMAN + :100: + : :---HBA_HORSE + :100: + : : :---MYG_PHYCA + : : : + : :100:---GLB5_PETMA + : : + : :---LGB2_LUPLU : :-----------HBB_HORSE : @@ -191,8 +218,8 @@ This quartet puzzling tree is not comple Quartet puzzling tree (in CLUSTAL W notation): -(HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, -HBA_HORSE)100)100,HBB_HORSE); +(HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, +HBB_HORSE); BIPARTITIONS @@ -200,23 +227,23 @@ BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****... : 1000 - **..... : 1000 - **..*** : 1000 + **..*** : 1000 (1.000) + ****... : 1000 (1.000) + **..... : 1000 (1.000) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 347 + ****.*. : 347 (0.347) Incongruent bipartitions not included in the consensus tree: -(bipartition with sequences in input order : number of times seen) +(bipartition with sequences in input order : number of times seen (and ratio)) - ****..* : 331 - ****.*. : 322 + *****.. : 341 (0.341) + ****..* : 312 (0.312) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -225,15 +252,15 @@ Branch lengths are computed using the se substitution and rate heterogeneity. - :-------------5 MYG_PHYCA - :-------8 - : :-------6 GLB5_PETMA - : : - : :------------------7 LGB2_LUPLU + :-3 HBA_HUMAN + :-----8 + : :--4 HBA_HORSE :-------10 - : : :-3 HBA_HUMAN - : :-----9 - : :--4 HBA_HORSE + : : :-------------5 MYG_PHYCA + : :-------9 + : :-------6 GLB5_PETMA + : : + : :------------------7 LGB2_LUPLU : :--2 HBB_HORSE : @@ -241,21 +268,21 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. -HBB_HUMAN 1 0.08 0.03102 8 0.44299 0.11946 -HBB_HORSE 2 0.11946 0.03740 9 0.25788 0.08204 +HBB_HUMAN 1 0.05028 0.03102 8 0.25788 0.08204 +HBB_HORSE 2 0.11946 0.03740 9 0.44299 0.11946 HBA_HUMAN 3 0.02934 0.02189 10 0.57110 0.10504 HBA_HORSE 4 0.09430 0.03146 -MYG_PHYCA 5 1.11230 0.17628 -GLB5_PETMA 6 0.59340 0.11994 11 iterations until convergence +MYG_PHYCA 5 1.11239 0.17630 +GLB5_PETMA 6 0.59341 0.11994 11 iterations until convergence LGB2_LUPLU 7 1.46501 0.22199 log L: -1699.78 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.08,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501) -100:0.44299,(HBA_HUMAN:0.02934,HBA_HORSE:0.09430)100:0.25788)100:0.57110, -HBB_HORSE:0.11946); +(HBB_HUMAN:0.05028,((HBA_HUMAN:0.02934,HBA_HORSE:0.09430)100:0.25788, +(MYG_PHYCA:1.11239,GLB5_PETMA:0.59341,LGB2_LUPLU:1.46501)100:0.44299) +100:0.57110,HBB_HORSE:0.11946); TIME STAMP --- a/tests/check-ut-pure-prot +++ b/tests/check-ut-pure-prot @@ -15,10 +15,36 @@ SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) + Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) +Concering parsimony informative sites there are: + +Number of parsimony informative sites: 78 (= 60.9% of all sites) + - fully informative sites: 12 (= 9.4% of all sites) + - partly informative sites: 66 (= 51.6% of all sites) +Number of parsimony uninformative sites: 50 (= 39.1% of all sites) + - variable, but uninformative sites: 43 (= 33.6% of all sites) + - completely constant sites: 7 (= 5.5% of all sites) + - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites) + + +For each sequence there are following numbers of parsimony (non-)informative site: + + informative sites non-informative sites + 1 HBB_HUMAN 72 ( 56.25%) 56 ( 43.75%) + 2 HBB_HORSE 75 ( 58.59%) 53 ( 41.41%) + 3 HBA_HUMAN 76 ( 59.38%) 52 ( 40.62%) + 4 HBA_HORSE 75 ( 58.59%) 53 ( 41.41%) + 5 MYG_PHYCA 41 ( 32.03%) 87 ( 67.97%) + 6 GLB5_PETMA 43 ( 33.59%) 85 ( 66.41%) + 7 LGB2_LUPLU 38 ( 29.69%) 90 ( 70.31%) + +Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ. + + SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) @@ -48,16 +74,16 @@ Amino acid frequencies (estimated from d AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) - gaps wildcards sum % sequence - HBB_HUMAN 0 0 0 0.00% - HBB_HORSE 0 0 0 0.00% - HBA_HUMAN 0 0 0 0.00% - HBA_HORSE 0 0 0 0.00% - MYG_PHYCA 0 0 0 0.00% - GLB5_PETMA 0 0 0 0.00% - LGB2_LUPLU 0 0 0 0.00% - ------------------------------------------------------- - Sum 0 0 0 0.00% + gaps wildcards sum % sequence + 1 HBB_HUMAN 0 0 0 0.00% + 2 HBB_HORSE 0 0 0 0.00% + 3 HBA_HUMAN 0 0 0 0.00% + 4 HBA_HORSE 0 0 0 0.00% + 5 MYG_PHYCA 0 0 0 0.00% + 6 GLB5_PETMA 0 0 0 0.00% + 7 LGB2_LUPLU 0 0 0 0.00% + ----------------------------------------------------------- + Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' @@ -72,20 +98,21 @@ information and had to be discarded from SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) - 5% chi-square test p-value - HBB_HUMAN passed 92.31% - HBB_HORSE passed 79.58% - HBA_HUMAN passed 93.09% - HBA_HORSE passed 81.20% - MYG_PHYCA passed 33.23% - GLB5_PETMA passed 19.11% - LGB2_LUPLU passed 41.67% - -The chi-square tests compares the amino acid composition of each sequence -to the frequency distribution assumed in the maximum likelihood model. + 5% chi-square test p-value chi2-value + 1 HBB_HUMAN passed 92.31% (11.02) + 2 HBB_HORSE passed 79.58% (13.79) + 3 HBA_HUMAN passed 93.09% (10.78) + 4 HBA_HORSE passed 81.20% (13.50) + 5 MYG_PHYCA passed 33.23% (21.08) + 6 GLB5_PETMA passed 19.11% (24.13) + 7 LGB2_LUPLU passed 41.67% (19.64) + +The chi-square tests with 19 degrees of freedom compares the +amino acid composition of each sequence to the frequency +distribution assumed in the maximum likelihood model. -WARNING: Result of chi-square test may not be valid because of small -maximum likelihood frequencies and short sequence length! +WARNING: Result of chi-square test may not be valid because of +small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES @@ -148,7 +175,7 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. HBB_HUMAN 1 0.04834 0.03148 8 0.28039 0.08746 -HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00141 +HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00100 HBA_HUMAN 3 0.02653 0.02208 10 0.40361 0.12824 HBA_HORSE 4 0.09440 0.03145 11 0.60481 0.11282 MYG_PHYCA 5 1.33106 0.21114 @@ -189,11 +216,11 @@ substitution and rate heterogeneity. branch length S.E. branch length S.E. HBB_HUMAN 1 0.04915 0.03158 8 0.28347 0.08778 -HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13088 -HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12 +HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13086 +HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12552 HBA_HORSE 4 0.09541 0.03153 11 0.60238 0.11261 MYG_PHYCA 5 1.33157 0.21115 -GLB5_PETMA 6 0.57473 0.13845 9 iterations until convergence +GLB5_PETMA 6 0.57473 0.13844 9 iterations until convergence LGB2_LUPLU 7 1.71340 0.27647 log L: -1699.00 @@ -286,10 +313,10 @@ COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH ------------------------------------------------------------------------------- - 1 -1699.50 0.49 1.0266 0.3020 + 0.4700 + 0.1881 + + - 2 -1699.00 0.00 <---- best 1.0000 + 1.0000 + 0.3650 + best - 3 -1699.32 0.32 1.3440 0.4030 + 0.4690 + 0.2588 + + - 4 -1699.50 0.49 1.0267 0.3070 + 0.4700 + 0.1881 + + + 1 -1699.50 0.49 1.0266 0.3150 + 0.4600 + 0.1871 + + + 2 -1699.00 0.00 <---- best 1.0000 + 1.0000 + 0.3643 + best + 3 -1699.32 0.32 1.3440 0.3950 + 0.4830 + 0.2614 + + + 4 -1699.50 0.49 1.0267 0.3350 + 0.4600 + 0.1871 + + The columns show the results and p-values of the following tests: 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa