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 1963 nucleotide sites Number of constant sites: 184 (= 9.4% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 0.70 (S.E. 0.03) Nucleotide frequencies (estimated from data set): pi(A) = 21.2% pi(C) = 27.7% pi(G) = 23.8% pi(T) = 27.4% Expected transition/transversion ratio: 0.71 Expected pyrimidine transition/purine transition ratio: 1.50 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value CELEGANS failed 0.00% [6] FLOWER failed 0.07% [7] FLY failed 0.00% [10] FROG failed 0.00% [11] DANIO passed 37.94% [10] TROUT passed 5.39% [8] MOUSE failed 2.05% [4] RAT failed 4.31% [3] HOMO failed 0.00% [6] PIG failed 0.00% [9] COW failed 0.00% [6] 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 20 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 CELEGANS 0.00000 0.49567 0.62098 0.68197 0.69383 0.57954 0.62376 0.62188 0.61482 0.49839 0.63820 FLOWER 0.49567 0.00000 0.66934 0.66060 0.74065 0.65885 0.56149 0.56580 0.57384 0.51658 0.60193 FLY 0.62098 0.66934 0.00000 0.57679 0.53180 0.50064 0.50727 0.47083 0.49171 0.42636 0.50771 FROG 0.68197 0.66060 0.57679 0.00000 0.54761 0.44525 0.44251 0.44070 0.44740 0.34330 0.48745 DANIO 0.69383 0.74065 0.53180 0.54761 0.00000 0.31879 0.43723 0.43882 0.45048 0.35206 0.46905 TROUT 0.57954 0.65885 0.50064 0.44525 0.31879 0.00000 0.38023 0.34472 0.35964 0.29504 0.38776 MOUSE 0.62376 0.56149 0.50727 0.44251 0.43723 0.38023 0.00000 0.03999 0.19444 0.17490 0.22282 RAT 0.62188 0.56580 0.47083 0.44070 0.43882 0.34472 0.03999 0.00000 0.19262 0.16839 0.21197 HOMO 0.61482 0.57384 0.49171 0.44740 0.45048 0.35964 0.19444 0.19262 0.00000 0.11699 0.17325 PIG 0.49839 0.51658 0.42636 0.34330 0.35206 0.29504 0.17490 0.16839 0.11699 0.00000 0.11550 COW 0.63820 0.60193 0.50771 0.48745 0.46905 0.38776 0.22282 0.21197 0.17325 0.11550 0.00000 Average distance (over all possible pairs of sequences): 0.44782 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: 20 (= 6.1%) 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. :---DANIO :-------------99: : :---TROUT : : :---MOUSE :-87: :----100: : : : :---RAT : : :-95: : : : : :---HOMO : : : : :-65: :-98: :-69: :-79: :---COW : : : : : : : :-------PIG : : : : : :---------------FROG : : : :-----------------------FLY : :---------------------------FLOWER : :---------------------------CELEGANS Quartet puzzling tree (in CLUSTAL W notation): (CELEGANS,(((DANIO,TROUT)99,(((MOUSE,RAT)100,((HOMO,COW)65, PIG)79)95,FROG)69)87,FLY)98,FLOWER); 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 ****..**** * : 992 **........ . : 981 ******.... . : 954 ***....... . : 868 ********.. . : 788 ***.**.... . : 685 ********.* . : 647 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *********. . : 308 ****...... . : 186 ******...* . : 173 ***...**** * : 113 **.*..**** * : 79 ******...* * : 36 ********.. * : 27 **..**.... . : 24 **.*...... . : 23 *.*....... . : 14 ******..*. * : 13 ****..**.. . : 12 *.*.****** * : 11 **..****** * : 9 ****....** * : 9 ****..***. * : 8 ***.*.**** * : 6 **....**** * : 5 ***.....** * : 4 **.*....** * : 2 (17 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. :-------5 DANIO :------12 : :------6 TROUT :---18 : : :-7 MOUSE : : :---13 : : : :-8 RAT : : :---16 : : : : :---9 HOMO : : : : :-14 : : : : : :----11 COW : : : :--15 : : : :--10 PIG : :--17 : :-----------4 FROG :--------19 : :----------3 FLY : :----------2 FLOWER : :---------1 CELEGANS branch length S.E. branch length S.E. CELEGANS 1 0.22925 0.02280 12 0.14315 0.02031 FLOWER 2 0.26879 0.02588 13 0.07360 0.01005 FLY 3 0.25875 0.02197 14 0.00703 0.00517 FROG 4 0.30390 0.02067 15 0.04672 0.00934 DANIO 5 0.19179 0.02103 16 0.07444 0.01410 TROUT 6 0.15580 0.01989 17 0.03382 0.01341 MOUSE 7 0.02027 0.00484 18 0.06991 0.01725 RAT 8 0.02040 0.00485 19 0.20452 0.02385 HOMO 9 0.08203 0.00978 PIG 10 0.04787 0.00998 11 iterations until convergence COW 11 0.09537 0.01057 log L: -10149.90 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (CELEGANS:0.22925,(((DANIO:0.19179,TROUT:0.15580)99:0.14315,(((MOUSE:0.02027, RAT:0.02040)100:0.07360,((HOMO:0.08203,COW:0.09537)65:0.00703,PIG:0.04787) 79:0.04672)95:0.07444,FROG:0.30390)69:0.03382)87:0.06991,FLY:0.25875) 98:0.20452,FLOWER:0.26879); TIME STAMP Date and time: Wed Jun 04 20:18:28 2003 Runtime: 8 seconds (= 0.1 minutes = 0.0 hours)