Description: Reduce decimals for testing Tests often fail because the last few decimals of the output depend on the compiler. This patch circumvents that. Author: Pranav Ballaney Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960760 Last-Update: 2020-06-11 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- a/tests/check-cons-pure-prot +++ b/tests/check-cons-pure-prot @@ -129,17 +129,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 -HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 -HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 -HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 -MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 -GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 -LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 - -Average distance (over all possible pairs of sequences): 1.73823 - minimum : 0.12147, maximum : 2.86187 - variance : 0.65214, std.dev. : 0.80755 +HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78 +HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86 +HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54 +HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51 +MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79 +GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18 +LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00 + +Average distance (over all possible pairs of sequences): 1.73 + minimum : 0.12, maximum : 2.86 + variance : 0.65, std.dev. : 0.80 RATE HETEROGENEITY @@ -188,21 +188,21 @@ Bipartitions included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 100 (1.000) - ****... : 100 (1.000) - **..... : 100 (1.000) + **..*** : 100 (1.00) + ****... : 100 (1.00) + **..... : 100 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..* : 40 (0.400) + ****..* : 40 (0.40) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 37 (0.370) - ****.*. : 23 (0.230) + *****.. : 37 (0.37) + ****.*. : 23 (0.23) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -227,21 +227,21 @@ branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04834 0.03148 8 0.28040 0.08746 -HBB_HORSE 2 0.12685 0.03876 9 0.40362 0.12823 -HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 -HBA_HORSE 4 0.09440 0.03145 -MYG_PHYCA 5 1.33099 0.21112 -GLB5_PETMA 6 0.70102 0.14139 10 iterations until convergence -LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 +HBB_HUMAN 1 0.04 0.03 8 0.28 0.08 +HBB_HORSE 2 0.12 0.03 9 0.40 0.12 +HBA_HUMAN 3 0.02 0.02 10 0.60 0.11 +HBA_HORSE 4 0.09 0.03 +MYG_PHYCA 5 1.33 0.21 +GLB5_PETMA 6 0.70 0.14 10 iterations until convergence +LGB2_LUPLU 7 1.76 0.28 log L: -1699.50 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04834,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)100:0.28040, -(MYG_PHYCA:1.33099,GLB5_PETMA:0.70102,LGB2_LUPLU:1.76831)100:0.40362) -100:0.60481,HBB_HORSE:0.12685); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.28, +(MYG_PHYCA:1.33,GLB5_PETMA:0.70,LGB2_LUPLU:1.76)100:0.40) +100:0.60,HBB_HORSE:0.12); TIME STAMP --- a/tests/check-lm-pure-prot +++ b/tests/check-lm-pure-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 -HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 -HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 -HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 -MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 -GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 -LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 +HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78 +HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86 +HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54 +HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51 +MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79 +GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18 +LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00 -Average distance (over all possible pairs of sequences): 1.73823 - minimum : 0.12147, maximum : 2.86187 - variance : 0.65214, std.dev. : 0.80755 +Average distance (over all possible pairs of sequences): 1.73 + minimum : 0.12, maximum : 2.86 + variance : 0.65, std.dev. : 0.80 RATE HETEROGENEITY --- a/tests/check-qp-clock +++ b/tests/check-qp-clock @@ -52,12 +52,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 2.98614 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 2.98614 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 2.98 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 2.98 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -126,26 +126,26 @@ substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 - 0.23734 -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 0.28562 - 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 0.28562 0.29036 0.00000 - 0.22452 -Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 - 0.00000 - -Average distance (over all possible pairs of sequences): 0.25459 - minimum : 0.13169, maximum : 0.33871 - variance : 0.00207, std.dev. : 0.04544 +Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22 + 0.23 +Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26 + 0.29 +Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17 + 0.23 +Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23 + 0.27 +Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28 + 0.27 +Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29 + 0.33 +Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00 + 0.22 +Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22 + 0.00 + +Average distance (over all possible pairs of sequences): 0.25 + minimum : 0.13, maximum : 0.33 + variance : 0.00, std.dev. : 0.04 RATE HETEROGENEITY @@ -239,40 +239,40 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 999 (0.999) - *..***** : 999 (0.999) - *...**.. : 730 (0.730) - ******.. : 711 (0.711) + ****..** : 999 (0.99) + *..***** : 999 (0.99) + *...**.. : 730 (0.73) + ******.. : 711 (0.71) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 466 (0.466) + *...**** : 466 (0.46) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 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) + ***.**.. : 333 (0.33) + *...**.* : 171 (0.17) + ***.**.* : 89 (0.08) + *..***.. : 80 (0.08) + *.....** : 79 (0.07) + *..*..** : 69 (0.06) + ****..*. : 51 (0.05) + *......* : 34 (0.03) + *..***.* : 30 (0.03) + ****.... : 28 (0.02) + ***.***. : 27 (0.02) + *..*.... : 22 (0.02) + *...***. : 20 (0.02) + ***..... : 19 (0.01) + *.....*. : 14 (0.01) + *..****. : 9 (0.00) + *..*..*. : 8 (0.00) + ***...** : 6 (0.00) + ***....* : 4 (0.00) + ****.**. : 1 (0.00) (1 other less frequent bipartitions not shown) @@ -301,22 +301,22 @@ 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 0.00572 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 -Philander 7 0.08995 0.03428 8 iterations until convergence -Bos 8 0.13479 0.04095 log L: -603.37 +Thylacinus 1 0.11 0.03 9 0.05 0.03 +Sarcophilu 2 0.13 0.03 10 0.08 0.03 +Dasyurus 3 0.00 0.01 11 0.04 0.02 +Echymipera 4 0.13 0.04 12 0.05 0.02 +Trichosuru 5 0.10 0.03 +Phalanger 6 0.12 0.04 +Philander 7 0.08 0.03 8 iterations until convergence +Bos 8 0.13 0.04 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05, +((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08, +Bos:0.13)71:0.04,Echymipera:0.13)73:0.05); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -350,30 +350,30 @@ 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 0.14706 0.750 9 0.04504 1.322 -Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 -Dasyurus 3 0.06189 0.092 11 0.03304 1.277 -Echymipera 4 0.12852 1.089 12 0.01851 2.948 -Trichosuru 5 0.10199 1.045 -Phalanger 6 0.10199 1.202 -Philander 7 0.09549 0.942 6 iterations until convergence -Bos 8 0.09549 1.412 log L: -610.75 +Thylacinus 1 0.14 0.75 9 0.04 1.32 +Sarcophilu 2 0.06 2.13 10 0.06 1.28 +Dasyurus 3 0.06 0.09 11 0.03 1.27 +Echymipera 4 0.12 1.08 12 0.01 2.94 +Trichosuru 5 0.10 1.04 +Phalanger 6 0.10 1.20 +Philander 7 0.09 0.94 6 iterations until convergence +Bos 8 0.09 1.41 log L: -610.75 height S.E. of node common to branches -0.10199 0.01922 9 5 6 -0.06189 0.01495 10 2 3 -0.09549 0.01498 11 7 8 -0.12852 0.01108 12 10 11 4 -0.14704 0.01235 1 9 12 -0.14705 0.02366 of root at branch 1 +0.10 0.01 9 5 6 +0.06 0.01 10 2 3 +0.09 0.01 11 7 8 +0.12 0.01 12 10 11 4 +0.14 0.01 1 9 12 +0.14 0.02 of root at branch 1 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.14,((Trichosuru:0.10,Phalanger:0.10)100:0.04 +,((Sarcophilu:0.06,Dasyurus:0.06)100:0.06,(Philander:0.09, +Bos:0.09)71:0.03,Echymipera:0.12)73:0.01):0.00); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-hky-clock-nucl +++ b/tests/check-qp-hky-clock-nucl @@ -52,12 +52,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 2.98614 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 2.98614 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 2.98 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 2.98 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -126,26 +126,26 @@ substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 - 0.23734 -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 0.28562 - 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 0.28562 0.29036 0.00000 - 0.22452 -Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 - 0.00000 - -Average distance (over all possible pairs of sequences): 0.25459 - minimum : 0.13169, maximum : 0.33871 - variance : 0.00207, std.dev. : 0.04544 +Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22 + 0.23 +Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26 + 0.29 +Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17 + 0.23 +Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23 + 0.27 +Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28 + 0.27 +Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29 + 0.33 +Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00 + 0.22 +Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22 + 0.00 + +Average distance (over all possible pairs of sequences): 0.25 + minimum : 0.13, maximum : 0.33 + variance : 0.00, std.dev. : 0.04 RATE HETEROGENEITY @@ -239,40 +239,40 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 999 (0.999) - *..***** : 999 (0.999) - *...**.. : 730 (0.730) - ******.. : 711 (0.711) + ****..** : 999 (0.99) + *..***** : 999 (0.99) + *...**.. : 730 (0.73) + ******.. : 711 (0.71) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 466 (0.466) + *...**** : 466 (0.46) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 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) + ***.**.. : 333 (0.33) + *...**.* : 171 (0.17) + ***.**.* : 89 (0.08) + *..***.. : 80 (0.08) + *.....** : 79 (0.07) + *..*..** : 69 (0.06) + ****..*. : 51 (0.05) + *......* : 34 (0.03) + *..***.* : 30 (0.03) + ****.... : 28 (0.02) + ***.***. : 27 (0.02) + *..*.... : 22 (0.02) + *...***. : 20 (0.02) + ***..... : 19 (0.01) + *.....*. : 14 (0.01) + *..****. : 9 (0.00) + *..*..*. : 8 (0.00) + ***...** : 6 (0.00) + ***....* : 4 (0.00) + ****.**. : 1 (0.00) (1 other less frequent bipartitions not shown) @@ -301,22 +301,22 @@ 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 0.00572 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 -Philander 7 0.08995 0.03428 8 iterations until convergence -Bos 8 0.13479 0.04095 log L: -603.37 +Thylacinus 1 0.11 0.03 9 0.05 0.03 +Sarcophilu 2 0.13 0.03 10 0.08 0.03 +Dasyurus 3 0.00 0.01 11 0.04 0.02 +Echymipera 4 0.13 0.04 12 0.05 0.02 +Trichosuru 5 0.10 0.03 +Phalanger 6 0.12 0.04 +Philander 7 0.08 0.03 8 iterations until convergence +Bos 8 0.13 0.04 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05, +((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08, +Bos:0.13)71:0.04,Echymipera:0.13)73:0.05); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -350,30 +350,30 @@ 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 0.14706 0.750 9 0.04504 1.322 -Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 -Dasyurus 3 0.06189 0.092 11 0.03304 1.277 -Echymipera 4 0.12852 1.089 12 0.01851 2.948 -Trichosuru 5 0.10199 1.045 -Phalanger 6 0.10199 1.202 -Philander 7 0.09549 0.942 6 iterations until convergence -Bos 8 0.09549 1.412 log L: -610.75 +Thylacinus 1 0.14 0.75 9 0.04 1.32 +Sarcophilu 2 0.06 2.13 10 0.06 1.28 +Dasyurus 3 0.06 0.09 11 0.03 1.27 +Echymipera 4 0.12 1.08 12 0.01 2.94 +Trichosuru 5 0.10 1.04 +Phalanger 6 0.10 1.20 +Philander 7 0.09 0.94 6 iterations until convergence +Bos 8 0.09 1.41 log L: -610.75 height S.E. of node common to branches -0.10199 0.01922 9 5 6 -0.06189 0.01495 10 2 3 -0.09549 0.01498 11 7 8 -0.12852 0.01108 12 10 11 4 -0.14704 0.01235 1 9 12 -0.14705 0.02366 of root at branch 1 +0.10 0.01 9 5 6 +0.06 0.01 10 2 3 +0.09 0.01 11 7 8 +0.12 0.01 12 10 11 4 +0.14 0.01 1 9 12 +0.14 0.02 of root at branch 1 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.14,((Trichosuru:0.10,Phalanger:0.10)100:0.04 +,((Sarcophilu:0.06,Dasyurus:0.06)100:0.06,(Philander:0.09, +Bos:0.09)71:0.03,Echymipera:0.12)73:0.01):0.00); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-hky-rhet-clock-nucl +++ b/tests/check-qp-hky-rhet-clock-nucl @@ -52,12 +52,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 4.86122 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 4.86122 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 4.86 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 4.86 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -126,26 +126,26 @@ substitution and rate heterogeneity. 8 -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): 0.48368 - minimum : 0.16226, maximum : 0.79725 - variance : 0.02195, std.dev. : 0.14817 +Thylacinus 0.00 0.43 0.31 0.42 0.48 0.46 0.36 + 0.45 +Sarcophilu 0.43 0.00 0.16 0.50 0.56 0.75 0.50 + 0.63 +Dasyurus 0.31 0.16 0.00 0.32 0.43 0.49 0.26 + 0.46 +Echymipera 0.42 0.50 0.32 0.00 0.56 0.75 0.35 + 0.54 +Trichosuru 0.48 0.56 0.43 0.56 0.00 0.32 0.56 + 0.51 +Phalanger 0.46 0.75 0.49 0.75 0.32 0.00 0.64 + 0.79 +Philander 0.36 0.50 0.26 0.35 0.56 0.64 0.00 + 0.40 +Bos 0.45 0.63 0.46 0.54 0.51 0.79 0.40 + 0.00 + +Average distance (over all possible pairs of sequences): 0.48 + minimum : 0.16, maximum : 0.79 + variance : 0.02, std.dev. : 0.14 RATE HETEROGENEITY @@ -157,10 +157,10 @@ Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.0007 0.2500 - 2 0.0674 0.2500 - 3 0.5911 0.2500 - 4 3.3407 0.2500 + 1 0.00 0.25 + 2 0.06 0.25 + 3 0.59 0.25 + 4 3.34 0.25 Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 and variance 3.91. @@ -260,40 +260,40 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 977 (0.977) - *..***** : 966 (0.966) - *...**.. : 591 (0.591) + ****..** : 977 (0.97) + *..***** : 966 (0.96) + *...**.. : 591 (0.59) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.* : 289 (0.289) - ***.**.. : 257 (0.257) + ***.**.* : 289 (0.28) + ***.**.. : 257 (0.25) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ******.. : 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) + ******.. : 256 (0.25) + ***.***. : 240 (0.24) + *...**** : 177 (0.17) + *...**.* : 148 (0.14) + *..***.* : 130 (0.13) + *..***.. : 102 (0.10) + *......* : 95 (0.09) + *..****. : 92 (0.09) + *...***. : 91 (0.09) + *..*..** : 82 (0.08) + ***..... : 70 (0.07) + ****..*. : 69 (0.06) + ****.... : 36 (0.03) + *..*.... : 36 (0.03) + *.....*. : 36 (0.03) + *.....** : 32 (0.03) + ***....* : 31 (0.03) + ***...** : 31 (0.03) + *..*...* : 26 (0.02) + *..*..*. : 26 (0.02) (29 other less frequent bipartitions not shown) @@ -322,14 +322,14 @@ branch length S.E. branch length S.E. -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 +Thylacinus 1 0.13 0.07 9 0.14 0.08 +Sarcophilu 2 0.16 0.05 10 0.15 0.07 +Dasyurus 3 0.00 0.00 11 0.07 0.07 +Echymipera 4 0.20 0.08 +Trichosuru 5 0.15 0.07 +Phalanger 6 0.18 0.08 +Philander 7 0.16 0.07 10 iterations until convergence +Bos 8 0.30 0.12 log L: -569.50 WARNING --- at least one branch length is close to an internal boundary! @@ -337,9 +337,9 @@ Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.13,(Trichosuru:0.15,Phalanger:0.18)98:0.14, +((Sarcophilu:0.16,Dasyurus:0.00)97:0.15,Echymipera:0.20, +Philander:0.16,Bos:0.30)59:0.07); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -373,29 +373,29 @@ 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 0.23195 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 +Thylacinus 1 0.23 0.57 9 0.16 0.86 +Sarcophilu 2 0.07 2.09 10 0.14 1.05 +Dasyurus 3 0.07 0.00 11 0.00 13.30 +Echymipera 4 0.22 0.90 +Trichosuru 5 0.17 0.88 +Phalanger 6 0.17 1.09 +Philander 7 0.22 0.71 13 iterations until convergence +Bos 8 0.22 1.35 log L: -574.14 height S.E. of node common to branches -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 +0.17 0.05 9 5 6 +0.07 0.02 10 2 3 +0.22 0.03 11 10 4 7 8 +0.23 0.04 9 11 1 +0.28 0.04 of root at branch 9 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -((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); +((Trichosuru:0.17,Phalanger:0.17)98:0.11,(((Sarcophilu:0.07, +Dasyurus:0.07)97:0.14,Echymipera:0.22,Philander:0.22, +Bos:0.22)59:0.00,Thylacinus:0.23):0.05); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-hky-rhet-nucl +++ b/tests/check-qp-hky-rhet-nucl @@ -52,12 +52,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 4.86122 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 4.86122 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 4.86 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 4.86 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -126,26 +126,26 @@ substitution and rate heterogeneity. 8 -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): 0.48368 - minimum : 0.16226, maximum : 0.79725 - variance : 0.02195, std.dev. : 0.14817 +Thylacinus 0.00 0.43 0.31 0.42 0.48 0.46 0.36 + 0.45 +Sarcophilu 0.43 0.00 0.16 0.50 0.56 0.75 0.50 + 0.63 +Dasyurus 0.31 0.16 0.00 0.32 0.43 0.49 0.26 + 0.46 +Echymipera 0.42 0.50 0.32 0.00 0.56 0.75 0.35 + 0.54 +Trichosuru 0.48 0.56 0.43 0.56 0.00 0.32 0.56 + 0.51 +Phalanger 0.46 0.75 0.49 0.75 0.32 0.00 0.64 + 0.79 +Philander 0.36 0.50 0.26 0.35 0.56 0.64 0.00 + 0.40 +Bos 0.45 0.63 0.46 0.54 0.51 0.79 0.40 + 0.00 + +Average distance (over all possible pairs of sequences): 0.48 + minimum : 0.16, maximum : 0.79 + variance : 0.02, std.dev. : 0.14 RATE HETEROGENEITY @@ -157,10 +157,10 @@ Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.0007 0.2500 - 2 0.0674 0.2500 - 3 0.5911 0.2500 - 4 3.3407 0.2500 + 1 0.00 0.25 + 2 0.06 0.25 + 3 0.59 0.25 + 4 3.34 0.25 Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 and variance 3.91. @@ -260,40 +260,40 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 977 (0.977) - *..***** : 966 (0.966) - *...**.. : 591 (0.591) + ****..** : 977 (0.97) + *..***** : 966 (0.96) + *...**.. : 591 (0.59) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.* : 289 (0.289) - ***.**.. : 257 (0.257) + ***.**.* : 289 (0.28) + ***.**.. : 257 (0.25) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ******.. : 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) + ******.. : 256 (0.25) + ***.***. : 240 (0.24) + *...**** : 177 (0.17) + *...**.* : 148 (0.14) + *..***.* : 130 (0.13) + *..***.. : 102 (0.10) + *......* : 95 (0.09) + *..****. : 92 (0.09) + *...***. : 91 (0.09) + *..*..** : 82 (0.08) + ***..... : 70 (0.07) + ****..*. : 69 (0.06) + ****.... : 36 (0.03) + *..*.... : 36 (0.03) + *.....*. : 36 (0.03) + *.....** : 32 (0.03) + ***....* : 31 (0.03) + ***...** : 31 (0.03) + *..*...* : 26 (0.02) + *..*..*. : 26 (0.02) (29 other less frequent bipartitions not shown) @@ -322,14 +322,14 @@ branch length S.E. branch length S.E. -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 +Thylacinus 1 0.13 0.07 9 0.14 0.08 +Sarcophilu 2 0.16 0.05 10 0.15 0.07 +Dasyurus 3 0.00 0.00 11 0.07 0.07 +Echymipera 4 0.20 0.08 +Trichosuru 5 0.15 0.07 +Phalanger 6 0.18 0.08 +Philander 7 0.16 0.07 10 iterations until convergence +Bos 8 0.30 0.12 log L: -569.50 WARNING --- at least one branch length is close to an internal boundary! @@ -337,9 +337,9 @@ Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.13,(Trichosuru:0.15,Phalanger:0.18)98:0.14, +((Sarcophilu:0.16,Dasyurus:0.00)97:0.15,Echymipera:0.20, +Philander:0.16,Bos:0.30)59:0.07); TIME STAMP --- a/tests/check-qp-jtt-prot +++ b/tests/check-qp-jtt-prot @@ -128,17 +128,17 @@ 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 1.25126 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 1.25126 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 - variance : 0.60537, std.dev. : 0.77805 +HBB_HUMAN 0.00 0.17 0.93 0.96 2.06 1.74 2.60 +HBB_HORSE 0.17 0.00 0.97 0.97 2.03 1.75 2.65 +HBA_HUMAN 0.93 0.97 0.00 0.12 1.93 1.25 2.51 +HBA_HORSE 0.96 0.97 0.12 0.00 1.99 1.34 2.47 +MYG_PHYCA 2.06 2.03 1.93 1.99 0.00 2.04 2.69 +GLB5_PETMA 1.74 1.75 1.25 1.34 2.04 0.00 2.23 +LGB2_LUPLU 2.60 2.65 2.51 2.47 2.69 2.23 0.00 + +Average distance (over all possible pairs of sequences): 1.69 + minimum : 0.12, maximum : 2.69 + variance : 0.60, std.dev. : 0.77 RATE HETEROGENEITY @@ -229,21 +229,21 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 480 (0.480) + *****.. : 480 (0.48) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 447 (0.447) - ****..* : 73 (0.073) + ****.*. : 447 (0.44) + ****..* : 73 (0.07) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -268,21 +268,21 @@ branch length S.E. branch length S.E. -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 0.09596 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 +HBB_HUMAN 1 0.04 0.03 8 0.25 0.08 +HBB_HORSE 2 0.12 0.03 9 0.42 0.12 +HBA_HUMAN 3 0.02 0.02 10 0.61 0.11 +HBA_HORSE 4 0.09 0.03 +MYG_PHYCA 5 1.31 0.21 +GLB5_PETMA 6 0.68 0.13 12 iterations until convergence +LGB2_LUPLU 7 1.72 0.26 log L: -1707.74 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.25, +(MYG_PHYCA:1.31,GLB5_PETMA:0.68,LGB2_LUPLU:1.72)100:0.42) +100:0.61,HBB_HORSE:0.12); TIME STAMP --- a/tests/check-qp-jtt-rhet-clock-prot +++ b/tests/check-qp-jtt-rhet-clock-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -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 +HBB_HUMAN 0.00 0.17 1.04 1.08 2.51 2.11 3.24 +HBB_HORSE 0.17 0.00 1.09 1.10 2.48 2.13 3.32 +HBA_HUMAN 1.04 1.09 0.00 0.12 2.35 1.45 3.25 +HBA_HORSE 1.08 1.10 0.12 0.00 2.43 1.57 3.14 +MYG_PHYCA 2.51 2.48 2.35 2.43 0.00 2.53 3.41 +GLB5_PETMA 2.11 2.13 1.45 1.57 2.53 0.00 2.84 +LGB2_LUPLU 3.24 3.32 3.25 3.14 3.41 2.84 0.00 + +Average distance (over all possible pairs of sequences): 2.07 + minimum : 0.12, maximum : 3.41 + variance : 1.03, std.dev. : 1.01 RATE HETEROGENEITY @@ -150,10 +150,10 @@ Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.3690 0.2500 - 2 0.7199 0.2500 - 3 1.1100 0.2500 - 4 1.8010 0.2500 + 1 0.36 0.25 + 2 0.71 0.25 + 3 1.11 0.25 + 4 1.80 0.25 Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 and variance 0.40. @@ -251,21 +251,21 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 480 (0.480) + *****.. : 480 (0.48) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 447 (0.447) - ****..* : 73 (0.073) + ****.*. : 447 (0.44) + ****..* : 73 (0.07) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -290,21 +290,21 @@ branch length S.E. branch length S.E. -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 +HBB_HUMAN 1 0.04 0.03 8 0.23 0.10 +HBB_HORSE 2 0.12 0.04 9 0.50 0.17 +HBA_HUMAN 3 0.01 0.02 10 0.74 0.14 +HBA_HORSE 4 0.10 0.03 +MYG_PHYCA 5 1.67 0.30 +GLB5_PETMA 6 0.80 0.18 11 iterations until convergence +LGB2_LUPLU 7 2.33 0.42 log L: -1701.58 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.01,HBA_HORSE:0.10)100:0.23, +(MYG_PHYCA:1.67,GLB5_PETMA:0.80,LGB2_LUPLU:2.33)100:0.50) +100:0.74,HBB_HORSE:0.12); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) @@ -336,28 +336,28 @@ 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 0.08750 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 +HBB_HUMAN 1 0.08 0.56 8 0.51 0.45 +HBB_HORSE 2 0.08 1.47 9 0.57 0.87 +HBA_HUMAN 3 0.06 0.30 10 0.49 1.52 +HBA_HORSE 4 0.06 1.62 +MYG_PHYCA 5 1.15 1.45 +GLB5_PETMA 6 1.15 0.69 7 iterations until convergence +LGB2_LUPLU 7 2.28 1.02 log L: -1708.22 height S.E. of node common to branches -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 +0.08 0.02 10 2 1 +0.06 0.01 8 3 4 +0.57 0.07 9 10 8 +1.15 0.11 7 9 5 6 +1.72 0.21 of root at branch 7 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(LGB2_LUPLU:1.72,(((HBB_HORSE:0.08,HBB_HUMAN:0.08):0.49 +,(HBA_HUMAN:0.06,HBA_HORSE:0.06)100:0.51):0.57,MYG_PHYCA:1.15, +GLB5_PETMA:1.15):0.56); MOLECULAR CLOCK LIKELIHOOD RATIO TEST --- a/tests/check-qp-jtt-rhet-prot +++ b/tests/check-qp-jtt-rhet-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -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 +HBB_HUMAN 0.00 0.17 1.04 1.08 2.51 2.11 3.24 +HBB_HORSE 0.17 0.00 1.09 1.10 2.48 2.13 3.32 +HBA_HUMAN 1.04 1.09 0.00 0.12 2.35 1.45 3.25 +HBA_HORSE 1.08 1.10 0.12 0.00 2.43 1.57 3.14 +MYG_PHYCA 2.51 2.48 2.35 2.43 0.00 2.53 3.41 +GLB5_PETMA 2.11 2.13 1.45 1.57 2.53 0.00 2.84 +LGB2_LUPLU 3.24 3.32 3.25 3.14 3.41 2.84 0.00 + +Average distance (over all possible pairs of sequences): 2.07 + minimum : 0.12, maximum : 3.41 + variance : 1.03, std.dev. : 1.01 RATE HETEROGENEITY @@ -150,10 +150,10 @@ Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability - 1 0.3690 0.2500 - 2 0.7199 0.2500 - 3 1.1100 0.2500 - 4 1.8010 0.2500 + 1 0.36 0.25 + 2 0.71 0.25 + 3 1.11 0.25 + 4 1.80 0.25 Categories 1-4 approximate a continuous Gamma-distribution with expectation 1 and variance 0.40. @@ -251,21 +251,21 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 480 (0.480) + *****.. : 480 (0.48) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 447 (0.447) - ****..* : 73 (0.073) + ****.*. : 447 (0.44) + ****..* : 73 (0.07) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -290,21 +290,21 @@ branch length S.E. branch length S.E. -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 +HBB_HUMAN 1 0.04 0.03 8 0.23 0.10 +HBB_HORSE 2 0.12 0.04 9 0.50 0.17 +HBA_HUMAN 3 0.01 0.02 10 0.74 0.14 +HBA_HORSE 4 0.10 0.03 +MYG_PHYCA 5 1.67 0.30 +GLB5_PETMA 6 0.80 0.18 11 iterations until convergence +LGB2_LUPLU 7 2.33 0.42 log L: -1701.58 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.01,HBA_HORSE:0.10)100:0.23, +(MYG_PHYCA:1.67,GLB5_PETMA:0.80,LGB2_LUPLU:2.33)100:0.50) +100:0.74,HBB_HORSE:0.12); TIME STAMP --- a/tests/check-qp-mtrev-prot +++ b/tests/check-qp-mtrev-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -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 1.55582 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 1.55582 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 - minimum : 0.13144, maximum : 3.63316 - variance : 1.07966, std.dev. : 1.03906 +HBB_HUMAN 0.00 0.19 1.12 1.16 2.59 2.15 3.47 +HBB_HORSE 0.19 0.00 1.17 1.20 2.74 2.18 3.63 +HBA_HUMAN 1.12 1.17 0.00 0.13 2.41 1.43 3.06 +HBA_HORSE 1.16 1.20 0.13 0.00 2.44 1.55 3.05 +MYG_PHYCA 2.59 2.74 2.41 2.44 0.00 2.62 3.47 +GLB5_PETMA 2.15 2.18 1.43 1.55 2.62 0.00 2.97 +LGB2_LUPLU 3.47 3.63 3.06 3.05 3.47 2.97 0.00 + +Average distance (over all possible pairs of sequences): 2.13 + minimum : 0.13, maximum : 3.63 + variance : 1.07, std.dev. : 1.03 RATE HETEROGENEITY @@ -229,24 +229,24 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - **..... : 1000 (1.000) - ****... : 957 (0.957) + **..*** : 1000 (1.00) + **..... : 1000 (1.00) + ****... : 957 (0.95) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 492 (0.492) + *****.. : 492 (0.49) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 476 (0.476) - ****..* : 31 (0.031) - **..*.* : 24 (0.024) - **..*.. : 19 (0.019) - **....* : 1 (0.001) + ****.*. : 476 (0.47) + ****..* : 31 (0.03) + **..*.* : 24 (0.02) + **..*.. : 19 (0.01) + **....* : 1 (0.00) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -271,21 +271,21 @@ branch length S.E. branch length S.E. -HBB_HUMAN 1 0.03472 0.03059 8 0.30126 0.09575 -HBB_HORSE 2 0.16246 0.04359 9 0.34149 0.13763 -HBA_HUMAN 3 0.04636 0.02527 10 0.70896 0.13056 -HBA_HORSE 4 0.08355 0.03082 -MYG_PHYCA 5 1.58550 0.26736 -GLB5_PETMA 6 0.88663 0.17157 10 iterations until convergence -LGB2_LUPLU 7 2.13259 0.35215 log L: -1736.55 +HBB_HUMAN 1 0.03 0.03 8 0.30 0.09 +HBB_HORSE 2 0.16 0.04 9 0.34 0.13 +HBA_HUMAN 3 0.04 0.02 10 0.70 0.13 +HBA_HORSE 4 0.08 0.03 +MYG_PHYCA 5 1.58 0.26 +GLB5_PETMA 6 0.88 0.17 10 iterations until convergence +LGB2_LUPLU 7 2.13 0.35 log L: -1736.55 Consensus tree with maximum likelihood branch lengths (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)96:0.34149) -100:0.70896,HBB_HORSE:0.16246); +(HBB_HUMAN:0.03,((HBA_HUMAN:0.04,HBA_HORSE:0.08)100:0.30, +(MYG_PHYCA:1.58,GLB5_PETMA:0.88,LGB2_LUPLU:2.13)96:0.34) +100:0.70,HBB_HORSE:0.16); TIME STAMP --- a/tests/check-qp-pure-bin +++ b/tests/check-qp-pure-bin @@ -101,15 +101,15 @@ substitution and rate heterogeneity. 5 -Gibbon 0.00000 0.05300 0.05176 0.05295 0.06171 -Human 0.05300 0.00000 0.00563 0.00903 0.04081 -Chimpanzee 0.05176 0.00563 0.00000 0.01018 0.03960 -Gorilla 0.05295 0.00903 0.01018 0.00000 0.03835 -Orangutan 0.06171 0.04081 0.03960 0.03835 0.00000 - -Average distance (over all possible pairs of sequences): 0.03630 - minimum : 0.00563, maximum : 0.06171 - variance : 0.00043, std.dev. : 0.02066 +Gibbon 0.00 0.05 0.05 0.05 0.06 +Human 0.05 0.00 0.00 0.00 0.04 +Chimpanzee 0.05 0.00 0.00 0.01 0.03 +Gorilla 0.05 0.00 0.01 0.00 0.03 +Orangutan 0.06 0.04 0.03 0.03 0.00 + +Average distance (over all possible pairs of sequences): 0.03 + minimum : 0.00, maximum : 0.06 + variance : 0.00, std.dev. : 0.02 RATE HETEROGENEITY @@ -193,8 +193,8 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *..** : 1000 (1.000) - *...* : 1000 (1.000) + *..** : 1000 (1.00) + *...* : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: @@ -221,18 +221,18 @@ branch length S.E. branch length S.E. -Gibbon 1 0.03803 0.00691 6 0.00339 0.00199 -Human 2 0.00240 0.00170 7 0.01106 0.00384 -Chimpanzee 3 0.00323 0.00196 -Gorilla 4 0.00353 0.00206 5 iterations until convergence -Orangutan 5 0.02357 0.00543 log L: -968.78 +Gibbon 1 0.03 0.00 6 0.00 0.00 +Human 2 0.00 0.00 7 0.01 0.00 +Chimpanzee 3 0.00 0.00 +Gorilla 4 0.00 0.00 5 iterations until convergence +Orangutan 5 0.02 0.00 log L: -968.78 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(Gibbon:0.03803,((Human:0.00240,Chimpanzee:0.00323)100:0.00339,Gorilla:0.00353) -100:0.01106,Orangutan:0.02357); +(Gibbon:0.03,((Human:0.00,Chimpanzee:0.00)100:0.00,Gorilla:0.00) +100:0.01,Orangutan:0.02); TIME STAMP --- a/tests/check-qp-pure-nucl +++ b/tests/check-qp-pure-nucl @@ -52,12 +52,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 2.98614 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 2.98614 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 2.98 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 2.98 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -126,26 +126,26 @@ substitution and rate heterogeneity. 8 -Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 - 0.23734 -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 0.28562 - 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 0.28562 0.29036 0.00000 - 0.22452 -Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 - 0.00000 - -Average distance (over all possible pairs of sequences): 0.25459 - minimum : 0.13169, maximum : 0.33871 - variance : 0.00207, std.dev. : 0.04544 +Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22 + 0.23 +Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26 + 0.29 +Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17 + 0.23 +Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23 + 0.27 +Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28 + 0.27 +Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29 + 0.33 +Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00 + 0.22 +Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22 + 0.00 + +Average distance (over all possible pairs of sequences): 0.25 + minimum : 0.13, maximum : 0.33 + variance : 0.00, std.dev. : 0.04 RATE HETEROGENEITY @@ -239,40 +239,40 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 999 (0.999) - *..***** : 999 (0.999) - *...**.. : 730 (0.730) - ******.. : 711 (0.711) + ****..** : 999 (0.99) + *..***** : 999 (0.99) + *...**.. : 730 (0.73) + ******.. : 711 (0.71) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *...**** : 466 (0.466) + *...**** : 466 (0.46) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 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) + ***.**.. : 333 (0.33) + *...**.* : 171 (0.17) + ***.**.* : 89 (0.08) + *..***.. : 80 (0.08) + *.....** : 79 (0.07) + *..*..** : 69 (0.06) + ****..*. : 51 (0.05) + *......* : 34 (0.03) + *..***.* : 30 (0.03) + ****.... : 28 (0.02) + ***.***. : 27 (0.02) + *..*.... : 22 (0.02) + *...***. : 20 (0.02) + ***..... : 19 (0.01) + *.....*. : 14 (0.01) + *..****. : 9 (0.00) + *..*..*. : 8 (0.00) + ***...** : 6 (0.00) + ***....* : 4 (0.00) + ****.**. : 1 (0.00) (1 other less frequent bipartitions not shown) @@ -301,22 +301,22 @@ 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 0.00572 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 -Philander 7 0.08995 0.03428 8 iterations until convergence -Bos 8 0.13479 0.04095 log L: -603.37 +Thylacinus 1 0.11 0.03 9 0.05 0.03 +Sarcophilu 2 0.13 0.03 10 0.08 0.03 +Dasyurus 3 0.00 0.01 11 0.04 0.02 +Echymipera 4 0.13 0.04 12 0.05 0.02 +Trichosuru 5 0.10 0.03 +Phalanger 6 0.12 0.04 +Philander 7 0.08 0.03 8 iterations until convergence +Bos 8 0.13 0.04 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05, +((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08, +Bos:0.13)71:0.04,Echymipera:0.13)73:0.05); TIME STAMP --- a/tests/check-qp-pure-prot +++ b/tests/check-qp-pure-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 -HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 -HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 -HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 -MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 -GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 -LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 - -Average distance (over all possible pairs of sequences): 1.73823 - minimum : 0.12147, maximum : 2.86187 - variance : 0.65214, std.dev. : 0.80755 +HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78 +HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86 +HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54 +HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51 +MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79 +GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18 +LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00 + +Average distance (over all possible pairs of sequences): 1.73 + minimum : 0.12, maximum : 2.86 + variance : 0.65, std.dev. : 0.80 RATE HETEROGENEITY @@ -229,10 +229,10 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) - *****.. : 821 (0.821) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) + *****.. : 821 (0.82) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: @@ -243,8 +243,8 @@ Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..* : 105 (0.105) - ****.*. : 74 (0.074) + ****..* : 105 (0.10) + ****.*. : 74 (0.07) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -269,21 +269,21 @@ 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 0.12552 -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 +HBB_HUMAN 1 0.04 0.03 8 0.28 0.08 +HBB_HORSE 2 0.12 0.03 9 0.18 0.13 +HBA_HUMAN 3 0.02 0.02 10 0.34 0.12 +HBA_HORSE 4 0.09 0.03 11 0.60 0.11 +MYG_PHYCA 5 1.33 0.21 +GLB5_PETMA 6 0.57 0.13 10 iterations until convergence +LGB2_LUPLU 7 1.71 0.27 log L: -1699.00 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.28, +((GLB5_PETMA:0.57,LGB2_LUPLU:1.71)82:0.18,MYG_PHYCA:1.33) +100:0.34)100:0.60,HBB_HORSE:0.12); TIME STAMP --- a/tests/check-qp-tn-nucl +++ b/tests/check-qp-tn-nucl @@ -53,12 +53,12 @@ Rate matrix R (parameters restricted to selected model): - A-C rate: 1.00000 - A-G rate: 1.54307 - A-T rate: 1.00000 - C-G rate: 1.00000 - C-T rate: 3.45671 - G-T rate: 1.00000 + A-C rate: 1.00 + A-G rate: 1.54 + A-T rate: 1.00 + C-G rate: 1.00 + C-T rate: 3.45 + G-T rate: 1.00 Nucleotide frequencies (estimated from data set): @@ -127,26 +127,26 @@ substitution and rate heterogeneity. 8 -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): 0.25896 - minimum : 0.13242, maximum : 0.34463 - variance : 0.00217, std.dev. : 0.04660 +Thylacinus 0.00 0.25 0.22 0.25 0.26 0.25 0.22 + 0.24 +Sarcophilu 0.25 0.00 0.13 0.27 0.28 0.33 0.26 + 0.30 +Dasyurus 0.22 0.13 0.00 0.20 0.25 0.25 0.17 + 0.24 +Echymipera 0.25 0.27 0.20 0.00 0.30 0.34 0.23 + 0.27 +Trichosuru 0.26 0.28 0.25 0.30 0.00 0.21 0.29 + 0.27 +Phalanger 0.25 0.33 0.25 0.34 0.21 0.00 0.29 + 0.33 +Philander 0.22 0.26 0.17 0.23 0.29 0.29 0.00 + 0.22 +Bos 0.24 0.30 0.24 0.27 0.27 0.33 0.22 + 0.00 + +Average distance (over all possible pairs of sequences): 0.25 + minimum : 0.13, maximum : 0.34 + variance : 0.00, std.dev. : 0.04 RATE HETEROGENEITY @@ -240,11 +240,11 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****..** : 1000 (1.000) - *..***** : 1000 (1.000) - *...**.. : 704 (0.704) - ******.. : 692 (0.692) - *...**** : 528 (0.528) + ****..** : 1000 (1.00) + *..***** : 1000 (1.00) + *...**.. : 704 (0.70) + ******.. : 692 (0.69) + *...**** : 528 (0.52) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: @@ -255,26 +255,26 @@ Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ***.**.. : 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) + ***.**.. : 191 (0.19) + *...**.* : 183 (0.18) + *..***.. : 128 (0.12) + ****..*. : 81 (0.08) + *.....** : 79 (0.07) + ***.**.* : 76 (0.07) + *..*..** : 68 (0.06) + ****.... : 58 (0.05) + *..*.... : 41 (0.04) + *......* : 39 (0.03) + *..***.* : 37 (0.03) + *...***. : 17 (0.01) + *.....*. : 16 (0.01) + ***..... : 14 (0.01) + ***.***. : 12 (0.01) + ***...** : 11 (0.01) + *..*..*. : 9 (0.00) + *..****. : 7 (0.00) + ***...*. : 4 (0.00) + *..*...* : 3 (0.00) (2 other less frequent bipartitions not shown) @@ -303,22 +303,22 @@ branch length S.E. branch length S.E. -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 +Thylacinus 1 0.11 0.03 9 0.06 0.03 +Sarcophilu 2 0.12 0.03 10 0.03 0.02 +Dasyurus 3 0.01 0.01 11 0.06 0.03 +Echymipera 4 0.13 0.04 12 0.02 0.02 +Trichosuru 5 0.10 0.03 13 0.04 0.02 +Phalanger 6 0.12 0.04 +Philander 7 0.08 0.03 8 iterations until convergence +Bos 8 0.13 0.04 log L: -599.59 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.06, +((Philander:0.08,Bos:0.13)69:0.03,((Sarcophilu:0.12, +Dasyurus:0.01)100:0.06,Echymipera:0.13)53:0.02)70:0.04); TIME STAMP --- a/tests/check-qp-vt-prot +++ b/tests/check-qp-vt-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.16783 0.85204 0.87347 1.69056 1.50964 2.05575 -HBB_HORSE 0.16783 0.00000 0.87363 0.87544 1.67978 1.52916 2.09374 -HBA_HUMAN 0.85204 0.87363 0.00000 0.11958 1.58540 1.13053 2.11864 -HBA_HORSE 0.87347 0.87544 0.11958 0.00000 1.64085 1.18694 2.01999 -MYG_PHYCA 1.69056 1.67978 1.58540 1.64085 0.00000 1.63531 2.09093 -GLB5_PETMA 1.50964 1.52916 1.13053 1.18694 1.63531 0.00000 1.84636 -LGB2_LUPLU 2.05575 2.09374 2.11864 2.01999 2.09093 1.84636 0.00000 - -Average distance (over all possible pairs of sequences): 1.40836 - minimum : 0.11958, maximum : 2.11864 - variance : 0.36159, std.dev. : 0.60133 +HBB_HUMAN 0.00 0.16 0.85 0.87 1.69 1.50 2.05 +HBB_HORSE 0.16 0.00 0.87 0.87 1.67 1.52 2.09 +HBA_HUMAN 0.85 0.87 0.00 0.11 1.58 1.13 2.11 +HBA_HORSE 0.87 0.87 0.11 0.00 1.64 1.18 2.01 +MYG_PHYCA 1.69 1.67 1.58 1.64 0.00 1.63 2.09 +GLB5_PETMA 1.50 1.52 1.13 1.18 1.63 0.00 1.84 +LGB2_LUPLU 2.05 2.09 2.11 2.01 2.09 1.84 0.00 + +Average distance (over all possible pairs of sequences): 1.40 + minimum : 0.11, maximum : 2.11 + variance : 0.36, std.dev. : 0.60 RATE HETEROGENEITY @@ -229,21 +229,21 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 347 (0.347) + ****.*. : 347 (0.34) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 341 (0.341) - ****..* : 312 (0.312) + *****.. : 341 (0.34) + ****..* : 312 (0.31) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -268,21 +268,21 @@ branch length S.E. branch length S.E. -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 1.02820 0.16336 -GLB5_PETMA 6 0.60660 0.11823 11 iterations until convergence -LGB2_LUPLU 7 1.38557 0.20879 log L: -1703.59 +HBB_HUMAN 1 0.04 0.03 8 0.25 0.08 +HBB_HORSE 2 0.12 0.03 9 0.42 0.11 +HBA_HUMAN 3 0.03 0.02 10 0.54 0.10 +HBA_HORSE 4 0.08 0.03 +MYG_PHYCA 5 1.02 0.16 +GLB5_PETMA 6 0.60 0.11 11 iterations until convergence +LGB2_LUPLU 7 1.38 0.20 log L: -1703.59 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.04,((HBA_HUMAN:0.03,HBA_HORSE:0.08)100:0.25, +(MYG_PHYCA:1.02,GLB5_PETMA:0.60,LGB2_LUPLU:1.38)100:0.42) +100:0.54,HBB_HORSE:0.12); TIME STAMP --- a/tests/check-qp-wag-prot +++ b/tests/check-qp-wag-prot @@ -128,17 +128,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.16900 0.89717 0.92939 1.84037 1.59398 2.23038 -HBB_HORSE 0.16900 0.00000 0.92202 0.93317 1.80081 1.60452 2.27765 -HBA_HUMAN 0.89717 0.92202 0.00000 0.12400 1.71106 1.17087 2.28564 -HBA_HORSE 0.92939 0.93317 0.12400 0.00000 1.77692 1.23977 2.22372 -MYG_PHYCA 1.84037 1.80081 1.71106 1.77692 0.00000 1.72932 2.25004 -GLB5_PETMA 1.59398 1.60452 1.17087 1.23977 1.72932 0.00000 1.91159 -LGB2_LUPLU 2.23038 2.27765 2.28564 2.22372 2.25004 1.91159 0.00000 - -Average distance (over all possible pairs of sequences): 1.50578 - minimum : 0.12400, maximum : 2.28564 - variance : 0.42979, std.dev. : 0.65558 +HBB_HUMAN 0.00 0.16 0.89 0.92 1.84 1.59 2.23 +HBB_HORSE 0.16 0.00 0.92 0.93 1.80 1.60 2.27 +HBA_HUMAN 0.89 0.92 0.00 0.12 1.71 1.17 2.28 +HBA_HORSE 0.92 0.93 0.12 0.00 1.77 1.23 2.22 +MYG_PHYCA 1.84 1.80 1.71 1.77 0.00 1.72 2.25 +GLB5_PETMA 1.59 1.60 1.17 1.23 1.72 0.00 1.91 +LGB2_LUPLU 2.23 2.27 2.28 2.22 2.25 1.91 0.00 + +Average distance (over all possible pairs of sequences): 1.50 + minimum : 0.12, maximum : 2.28 + variance : 0.42, std.dev. : 0.65 RATE HETEROGENEITY @@ -229,21 +229,21 @@ Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen (and ratio)) - **..*** : 1000 (1.000) - ****... : 1000 (1.000) - **..... : 1000 (1.000) + **..*** : 1000 (1.00) + ****... : 1000 (1.00) + **..... : 1000 (1.00) Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - ****.*. : 347 (0.347) + ****.*. : 347 (0.34) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen (and ratio)) - *****.. : 341 (0.341) - ****..* : 312 (0.312) + *****.. : 341 (0.34) + ****..* : 312 (0.31) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) @@ -268,21 +268,21 @@ branch length S.E. branch length S.E. -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 1.11239 0.17630 -GLB5_PETMA 6 0.59341 0.11994 11 iterations until convergence -LGB2_LUPLU 7 1.46501 0.22199 log L: -1699.78 +HBB_HUMAN 1 0.05 0.03 8 0.25 0.08 +HBB_HORSE 2 0.11 0.03 9 0.44 0.11 +HBA_HUMAN 3 0.02 0.02 10 0.57 0.10 +HBA_HORSE 4 0.09 0.03 +MYG_PHYCA 5 1.11 0.17 +GLB5_PETMA 6 0.59 0.11 11 iterations until convergence +LGB2_LUPLU 7 1.46 0.22 log L: -1699.78 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(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); +(HBB_HUMAN:0.05,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.25, +(MYG_PHYCA:1.11,GLB5_PETMA:0.59,LGB2_LUPLU:1.46)100:0.44) +100:0.57,HBB_HORSE:0.11); TIME STAMP --- a/tests/check-ut-pure-prot +++ b/tests/check-ut-pure-prot @@ -129,17 +129,17 @@ substitution and rate heterogeneity. 7 -HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 -HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 -HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 -HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 -MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 -GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 -LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 - -Average distance (over all possible pairs of sequences): 1.73823 - minimum : 0.12147, maximum : 2.86187 - variance : 0.65214, std.dev. : 0.80755 +HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78 +HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86 +HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54 +HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51 +MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79 +GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18 +LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00 + +Average distance (over all possible pairs of sequences): 1.73 + minimum : 0.12, maximum : 2.86 + variance : 0.65, std.dev. : 0.80 RATE HETEROGENEITY @@ -174,13 +174,13 @@ 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 0.00100 -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 -GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence -LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50 +HBB_HUMAN 1 0.04 0.03 8 0.28 0.08 +HBB_HORSE 2 0.12 0.03 9 0.00 9.00 +HBA_HUMAN 3 0.02 0.02 10 0.40 0.12 +HBA_HORSE 4 0.09 0.03 11 0.60 0.11 +MYG_PHYCA 5 1.33 0.21 +GLB5_PETMA 6 0.70 0.14 9 iterations until convergence +LGB2_LUPLU 7 1.76 0.28 log L: -1699.50 WARNING --- at least one branch length is close to an internal boundary! @@ -188,9 +188,9 @@ Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04834,HBB_HORSE:0.12686,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440) -:0.28039,((MYG_PHYCA:1.33106,GLB5_PETMA:0.70107):0.00001,LGB2_LUPLU:1.76830) -:0.40361):0.60481); +(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09) +:0.28,((MYG_PHYCA:1.33,GLB5_PETMA:0.70):0.00,LGB2_LUPLU:1.76) +:0.40):0.60); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) @@ -215,21 +215,21 @@ 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 0.13086 -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 0.13844 9 iterations until convergence -LGB2_LUPLU 7 1.71340 0.27647 log L: -1699.00 +HBB_HUMAN 1 0.04 0.03 8 0.28 0.08 +HBB_HORSE 2 0.12 0.03 9 0.18 0.13 +HBA_HUMAN 3 0.02 0.02 10 0.34 0.12 +HBA_HORSE 4 0.09 0.03 11 0.60 0.11 +MYG_PHYCA 5 1.33 0.21 +GLB5_PETMA 6 0.57 0.13 9 iterations until convergence +LGB2_LUPLU 7 1.71 0.27 log L: -1699.00 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04915,HBB_HORSE:0.12604,((HBA_HUMAN:0.02555,HBA_HORSE:0.09541) -:0.28347,(MYG_PHYCA:1.33157,(GLB5_PETMA:0.57473,LGB2_LUPLU:1.71340) -:0.18149):0.34695):0.60238); +(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09) +:0.28,(MYG_PHYCA:1.33,(GLB5_PETMA:0.57,LGB2_LUPLU:1.71) +:0.18):0.34):0.60); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) @@ -254,21 +254,21 @@ branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04869 0.03153 8 0.27871 0.08717 -HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15661 -HBA_HUMAN 3 0.02634 0.02204 10 0.39110 0.12780 -HBA_HORSE 4 0.09459 0.03147 11 0.60627 0.11286 -MYG_PHYCA 5 1.22880 0.20960 -GLB5_PETMA 6 0.69972 0.14141 11 iterations until convergence -LGB2_LUPLU 7 1.68480 0.28106 log L: -1699.32 +HBB_HUMAN 1 0.04 0.03 8 0.27 0.08 +HBB_HORSE 2 0.12 0.03 9 0.12 0.15 +HBA_HUMAN 3 0.02 0.02 10 0.39 0.12 +HBA_HORSE 4 0.09 0.03 11 0.60 0.11 +MYG_PHYCA 5 1.22 0.20 +GLB5_PETMA 6 0.69 0.14 11 iterations until convergence +LGB2_LUPLU 7 1.68 0.28 log L: -1699.32 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04869,HBB_HORSE:0.12653,((HBA_HUMAN:0.02634,HBA_HORSE:0.09459) -:0.27871,((MYG_PHYCA:1.22880,LGB2_LUPLU:1.68480):0.12334,GLB5_PETMA:0.69972) -:0.39110):0.60627); +(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09) +:0.27,((MYG_PHYCA:1.22,LGB2_LUPLU:1.68):0.12,GLB5_PETMA:0.69) +:0.39):0.60); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) @@ -293,30 +293,30 @@ branch length S.E. branch length S.E. -HBB_HUMAN 1 0.04834 0.03148 8 0.40364 0.12824 -HBB_HORSE 2 0.12685 0.03876 9 0.28040 0.08746 -HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 -HBA_HORSE 4 0.09440 0.03145 -MYG_PHYCA 5 1.33095 0.21112 -GLB5_PETMA 6 0.70107 0.14140 10 iterations until convergence -LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 +HBB_HUMAN 1 0.04 0.03 8 0.40 0.12 +HBB_HORSE 2 0.12 0.03 9 0.28 0.08 +HBA_HUMAN 3 0.02 0.02 10 0.60 0.11 +HBA_HORSE 4 0.09 0.03 +MYG_PHYCA 5 1.33 0.21 +GLB5_PETMA 6 0.70 0.14 10 iterations until convergence +LGB2_LUPLU 7 1.76 0.28 log L: -1699.50 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): -(HBB_HUMAN:0.04834,((MYG_PHYCA:1.33095,GLB5_PETMA:0.70107,LGB2_LUPLU:1.76831) -:0.40364,(HBA_HUMAN:0.02653,HBA_HORSE:0.09440):0.28040):0.60481,HBB_HORSE:0.12685); +(HBB_HUMAN:0.04,((MYG_PHYCA:1.33,GLB5_PETMA:0.70,LGB2_LUPLU:1.76) +:0.40,(HBA_HUMAN:0.02,HBA_HORSE:0.09):0.28):0.60,HBB_HORSE:0.12); 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 0.3150 + 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 + + + 1 -1699.50 0.49 1.02 0.31 + 0.46 + 0.18 + + + 2 -1699.00 0.00 <---- best 1.00 + 1.00 + 0.36 + best + 3 -1699.32 0.32 1.34 0.39 + 0.48 + 0.26 + + + 4 -1699.50 0.49 1.02 0.33 + 0.46 + 0.18 + + The columns show the results and p-values of the following tests: 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa --- a/tests/cons-pure-prot.test +++ b/tests/cons-pure-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/lm-pure-prot.test +++ b/tests/lm-pure-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-clock.test +++ b/tests/qp-clock.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-hky-clock-nucl.test +++ b/tests/qp-hky-clock-nucl.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-hky-rhet-clock-nucl.test +++ b/tests/qp-hky-rhet-clock-nucl.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-hky-rhet-nucl.test +++ b/tests/qp-hky-rhet-nucl.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-jtt-prot.test +++ b/tests/qp-jtt-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-jtt-rhet-clock-prot.test +++ b/tests/qp-jtt-rhet-clock-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-jtt-rhet-prot.test +++ b/tests/qp-jtt-rhet-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-mtrev-prot.test +++ b/tests/qp-mtrev-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-pure-bin.test +++ b/tests/qp-pure-bin.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-pure-nucl.test +++ b/tests/qp-pure-nucl.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-pure-prot.test +++ b/tests/qp-pure-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-tn-nucl.test +++ b/tests/qp-tn-nucl.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-vt-prot.test +++ b/tests/qp-vt-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/qp-wag-prot.test +++ b/tests/qp-wag-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/template-test +++ b/tests/template-test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? --- a/tests/ut-pure-prot.test +++ b/tests/ut-pure-prot.test @@ -229,6 +229,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > check-${TEST_PREF} exit 0 else @@ -238,6 +239,7 @@ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed -e "s/$VVV//g" \ + | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$?