TREE-PUZZLE 5.2 Input file name: /usr/share/tree-puzzle/data/atp6.a Type of analysis: tree reconstruction 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 226 amino acid sites Number of constant sites: 102 (= 45.1% of all sites) Number of site patterns: 127 Number of constant site patterns: 18 (= 14.2% of all site patterns) SUBSTITUTION PROCESS Model of substitution: mtREV24 (Adachi-Hasegawa 1996) Amino acid frequencies (estimated from data set): pi(A) = 7.1% pi(R) = 2.2% pi(N) = 4.2% pi(D) = 0.6% pi(C) = 0.2% pi(Q) = 3.4% pi(E) = 1.5% pi(G) = 4.3% pi(H) = 3.0% pi(I) = 11.6% pi(L) = 19.5% pi(K) = 2.0% pi(M) = 5.8% pi(F) = 5.3% pi(P) = 6.4% pi(S) = 6.6% pi(T) = 9.9% pi(W) = 1.5% pi(Y) = 1.1% pi(V) = 3.9% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence chicken 0 0 0 0.00% cat 0 0 0 0.00% horse 0 0 0 0.00% mouse 0 0 0 0.00% opossum 0 0 0 0.00% platypus 0 0 0 0.00% rat 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 226 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 chicken passed 48.08% cat passed 100.00% horse passed 100.00% mouse passed 99.99% opossum passed 99.98% platypus passed 100.00% rat passed 99.78% The chi-square tests 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 chicken 0.00000 0.72667 0.72431 0.79989 0.64439 0.62225 0.85605 cat 0.72667 0.00000 0.09376 0.19385 0.34141 0.32597 0.22530 horse 0.72431 0.09376 0.00000 0.18856 0.33766 0.31976 0.22026 mouse 0.79989 0.19385 0.18856 0.00000 0.36030 0.33099 0.05405 opossum 0.64439 0.34141 0.33766 0.36030 0.00000 0.16376 0.38421 platypus 0.62225 0.32597 0.31976 0.33099 0.16376 0.00000 0.36777 rat 0.85605 0.22530 0.22026 0.05405 0.38421 0.36777 0.00000 Average distance (over all possible pairs of sequences): 0.39434 minimum : 0.05405, maximum : 0.85605 variance : 0.05672, std.dev. : 0.23816 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- chicken 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 cat 18 [ 90.00%] 0 [ 0.00%] 2 [ 10.00%] 20 horse 18 [ 90.00%] 0 [ 0.00%] 2 [ 10.00%] 20 mouse 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 opossum 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 platypus 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 rat 18 [ 90.00%] 0 [ 0.00%] 2 [ 10.00%] 20 -------------------------------------------------------------------------- #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 relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 32 (= 91.4%) Partly resolved quartets: 0 (= 0.0%) Unresolved quartets: 3 (= 8.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is completely resolved. :---mouse :100: : :---rat :100: : : :---cat : :-90: : :---horse : : :---opossum :-----96: : :---platypus : :-----------chicken Quartet puzzling tree (in CLUSTAL W notation): (chicken,((mouse,rat)100,(cat,horse)90)100,(opossum,platypus)96); 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) ***.**. : 1000 *...**. : 1000 ****..* : 958 *..**** : 899 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) None (No congruent split not included) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) **..**. : 53 *.*.**. : 48 *...*.. : 27 *....*. : 15 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-4 mouse :-----8 : :--7 rat :-----10 : : :--2 cat : :---9 : :--3 horse : : :----5 opossum :---11 : :---6 platypus : :-----------------1 chicken branch length S.E. branch length S.E. chicken 1 0.52729 0.06690 8 0.12131 0.02679 cat 2 0.04703 0.01648 9 0.03381 0.01668 horse 3 0.04655 0.01651 10 0.13412 0.03200 mouse 4 0.00542 0.00697 11 0.06973 0.02559 opossum 5 0.10146 0.02472 platypus 6 0.06597 0.02134 8 iterations until convergence rat 7 0.04877 0.01533 log L: -1618.09 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (chicken:0.52729,((mouse:0.00542,rat:0.04877)100:0.12131,(cat:0.04703, horse:0.04655)90:0.03381)100:0.13412,(opossum:0.10146,platypus:0.06597) 96:0.06973); TIME STAMP Date and time: Fri May 25 15:57:20 2007 Runtime (excl. input) : 0 seconds (= 0.0 minutes = 0.0 hours) Runtime (incl. input) : 8 seconds (= 0.1 minutes = 0.0 hours)