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TREE-PUZZLE
Input file name: lm-pure-prot.prot
Type of analysis: likelihood mapping
Parameter estimation: approximate (faster)
Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation)
Standard errors (S.E.) are obtained by the curvature method.
The upper and lower bounds of an approximate 95% confidence interval
for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E.
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)
Amino acid frequencies (estimated from data set):
pi(A) = 12.2%
pi(R) = 2.3%
pi(N) = 3.0%
pi(D) = 4.9%
pi(C) = 0.7%
pi(Q) = 2.3%
pi(E) = 5.4%
pi(G) = 6.0%
pi(H) = 5.8%
pi(I) = 2.7%
pi(L) = 12.5%
pi(K) = 9.3%
pi(M) = 1.3%
pi(F) = 4.9%
pi(P) = 2.6%
pi(S) = 6.7%
pi(T) = 4.5%
pi(W) = 1.3%
pi(Y) = 2.2%
pi(V) = 9.4%
AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER)
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'
characters ('X', '?', etc.) and their percentage of the 128 columns
in the alignment.
Sequences with more than 50% ambiguous characters are marked with a '!' and
should be checked, whether they have sufficient overlap to other sequences.
Sequences with 100% ambiguous characters do not hold any phylogenetic
information and had to be discarded from the analysis.
SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER)
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!
IDENTICAL SEQUENCES
The sequences in each of the following groups are all identical. To speed
up computation please remove all but one of each group from the data set.
All sequences are unique.
MAXIMUM LIKELIHOOD DISTANCES
Maximum likelihood distances are computed using the selected model of
substitution and rate heterogeneity.
7
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
Model of rate heterogeneity: uniform rate
LIKELIHOOD MAPPING ANALYSIS
Number of quartets: 35 (all possible)
Quartet trees are based on approximate maximum likelihood values
using the selected model of substitution and rate heterogeneity.
Sequences are not grouped in clusters.
LIKELIHOOD MAPPING STATISTICS
(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:
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
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