PUZZLE 4.0.2 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: 11 sequences with 3436 nucleotide sites Number of constant sites: 46 (= 1.3% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 0.98 (S.E. 0.05) Nucleotide frequencies (estimated from data set): pi(A) = 27.3% pi(C) = 23.4% pi(G) = 27.0% pi(T) = 22.4% Expected transition/transversion ratio: 0.99 Expected pyrimidine transition/purine transition ratio: 0.71 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value PIG failed 0.00% [10] TROUT passed 20.50% [2] HOMO failed 0.02% [6] COW failed 0.00% [7] MOUSE failed 0.67% [5] RAT failed 0.01% [5] FROG failed 0.00% [1] DANIO passed 7.47% [3] FLY passed 34.19% [2] CELEGANS failed 0.03% [4] FLOWER failed 1.71% [7] The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. The number in square brackets indicates how often each sequence is involved in one of the 13 completely unresolved quartets of the quartet puzzling tree search. 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. 11 PIG 0.00000 0.34389 0.53797 0.52089 0.50578 0.50962 0.55191 0.66737 0.74781 0.73676 0.80082 TROUT 0.34389 0.00000 0.17146 0.17577 0.18623 0.17501 0.25331 0.29263 0.29285 0.34384 0.33567 HOMO 0.53797 0.17146 0.00000 0.09266 0.14256 0.13866 0.26671 0.22213 0.33267 0.37516 0.38599 COW 0.52089 0.17577 0.09266 0.00000 0.12545 0.11858 0.24098 0.23676 0.27072 0.34710 0.34740 MOUSE 0.50578 0.18623 0.14256 0.12545 0.00000 0.05693 0.26626 0.22179 0.35906 0.36762 0.40371 RAT 0.50962 0.17501 0.13866 0.11858 0.05693 0.00000 0.29834 0.22344 0.35273 0.37670 0.40277 FROG 0.55191 0.25331 0.26671 0.24098 0.26626 0.29834 0.00000 0.21415 0.37471 0.39386 0.41021 DANIO 0.66737 0.29263 0.22213 0.23676 0.22179 0.22344 0.21415 0.00000 0.32151 0.38851 0.42630 FLY 0.74781 0.29285 0.33267 0.27072 0.35906 0.35273 0.37471 0.32151 0.00000 0.35809 0.40569 CELEGANS 0.73676 0.34384 0.37516 0.34710 0.36762 0.37670 0.39386 0.38851 0.35809 0.00000 0.38608 FLOWER 0.80082 0.33567 0.38599 0.34740 0.40371 0.40277 0.41021 0.42630 0.40569 0.38608 0.00000 Average distance (over all possible pairs of sequences): 0.34185 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: 330 Unresolved quartets: 13 (= 3.9%) 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. :---CELEGANS :-99: :-97: :---FLOWER : : :-93: :-------FLY : : : : :---FROG : :-----97: :-99: :---DANIO : : : : :---MOUSE : : :-98: : : : :---RAT : :-----79: : : :---HOMO : :-85: : :---COW : :-------------------TROUT : :-------------------PIG Quartet puzzling tree (in CLUSTAL W notation): (PIG,((((CELEGANS,FLOWER)99,FLY)97,(FROG,DANIO)97)93,((MOUSE, RAT)98,(HOMO,COW)85)79)99,TROUT); 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) **........ . : 994 *********. . : 988 ****..**** * : 981 ********.. . : 974 ******..** * : 974 ******.... . : 926 **..****** * : 845 **....**** * : 788 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **..**.... . : 106 **.*..**** * : 102 ****...... . : 72 **......** * : 50 *******... . : 23 **.*...... . : 23 ******...* * : 21 ***.**.... . : 20 ***...**** * : 17 **....**.. . : 17 **.***.... . : 14 **..*..... . : 13 ********.. * : 10 ***....... . : 8 **.......* * : 8 *.****.... . : 4 ****....** * : 3 **...*.... . : 3 ******.*.. . : 3 **..*.**** * : 2 (10 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :------10 CELEGANS :---12 : :--------11 FLOWER :----13 : :------9 FLY :--15 : : :-----7 FROG : :--14 : :----8 DANIO :-19 : : :-5 MOUSE : : :--16 : : : :--6 RAT : :--18 : : :--3 HOMO : :-17 : :--4 COW : :---2 TROUT : :-------------1 PIG branch length S.E. branch length S.E. PIG 1 0.36985 0.03830 12 0.06232 0.01115 TROUT 2 0.07952 0.01407 13 0.09591 0.01195 HOMO 3 0.04806 0.00747 14 0.05008 0.00966 COW 4 0.05427 0.00981 15 0.03446 0.00907 MOUSE 5 0.02947 0.00493 16 0.04827 0.00738 RAT 6 0.03029 0.00509 17 0.02801 0.00677 FROG 7 0.12123 0.01157 18 0.05592 0.00915 DANIO 8 0.10869 0.01351 19 0.00268 0.01164 FLY 9 0.16162 0.01379 CELEGANS 10 0.17671 0.01525 23 iterations until convergence FLOWER 11 0.21564 0.01686 log L: -11946.62 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (PIG:0.36985,((((CELEGANS:0.17671,FLOWER:0.21564)99:0.06232,FLY:0.16162) 97:0.09591,(FROG:0.12123,DANIO:0.10869)97:0.05008)93:0.03446,((MOUSE:0.02947, RAT:0.03029)98:0.04827,(HOMO:0.04806,COW:0.05427)85:0.02801)79:0.05592) 99:0.00268,TROUT:0.07952); TIME STAMP Date and time: Wed Jun 04 20:29:36 2003 Runtime: 9 seconds (= 0.1 minutes = 0.0 hours)