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 1275 nucleotide sites Number of constant sites: 66 (= 5.2% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 0.93 (S.E. 0.05) Nucleotide frequencies (estimated from data set): pi(A) = 27.2% pi(C) = 21.5% pi(G) = 25.0% pi(T) = 26.3% Expected transition/transversion ratio: 0.92 Expected pyrimidine transition/purine transition ratio: 0.83 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value COW failed 0.74% [19] FLY failed 1.87% [7] CELEGANS passed 35.39% [9] FLOWER failed 3.49% [4] SOY passed 38.33% [2] HOMO passed 6.00% [6] PIG passed 9.95% [5] MOUSE passed 92.08% [7] RAT passed 87.88% [7] TROUT failed 0.19% [3] FROG passed 98.89% [11] 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 COW 0.00000 0.86970 0.94246 0.89238 0.93710 0.62624 0.50276 0.55013 0.58138 0.72200 0.69414 FLY 0.86970 0.00000 0.55914 0.55255 0.57013 0.48638 0.43751 0.46627 0.48483 0.39952 0.50075 CELEGANS 0.94246 0.55914 0.00000 0.57627 0.62651 0.59208 0.50202 0.53615 0.54837 0.54795 0.56772 FLOWER 0.89238 0.55255 0.57627 0.00000 0.27180 0.49917 0.39769 0.47033 0.48281 0.47093 0.55566 SOY 0.93710 0.57013 0.62651 0.27180 0.00000 0.51883 0.41147 0.49651 0.51002 0.47444 0.49440 HOMO 0.62624 0.48638 0.59208 0.49917 0.51883 0.00000 0.06917 0.10128 0.11850 0.23977 0.28529 PIG 0.50276 0.43751 0.50202 0.39769 0.41147 0.06917 0.00000 0.09899 0.12151 0.24150 0.29495 MOUSE 0.55013 0.46627 0.53615 0.47033 0.49651 0.10128 0.09899 0.00000 0.04883 0.23015 0.27594 RAT 0.58138 0.48483 0.54837 0.48281 0.51002 0.11850 0.12151 0.04883 0.00000 0.25004 0.29339 TROUT 0.72200 0.39952 0.54795 0.47093 0.47444 0.23977 0.24150 0.23015 0.25004 0.00000 0.24027 FROG 0.69414 0.50075 0.56772 0.55566 0.49440 0.28529 0.29495 0.27594 0.29339 0.24027 0.00000 Average distance (over all possible pairs of sequences): 0.45884 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. :---FLOWER :100: : :---SOY :100: : : :---FLY : :-92: :-88: :---CELEGANS : : : : :---TROUT : :-----79: : :---FROG : : :---MOUSE : :-96: : :-77: :---RAT : : : :-72: :-------HOMO : : : :-----------PIG : :---------------COW Quartet puzzling tree (in CLUSTAL W notation): (COW,(((FLOWER,SOY)100,(FLY,CELEGANS)92)100,(TROUT,FROG)79)88, (((MOUSE,RAT)96,HOMO)77,PIG)72); 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 *....***** * : 995 *******..* * : 959 *..******* * : 923 *....****. . : 883 *********. . : 789 *****.*..* * : 771 *****....* * : 716 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *.....*... . : 216 *****..*** * : 174 *....****. * : 139 **...***** * : 70 *....***** . : 68 *****..... . : 57 *....*.**. . : 52 *....**... . : 46 *........* * : 35 *****.**.* * : 33 *......**. . : 10 *......... * : 8 *****.*... . : 8 *....*.... . : 7 *****....* . : 7 *.*..***** * : 7 ***..***** . : 5 *****.*.** * : 4 ******...* * : 3 *.....*..* * : 3 (8 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. :----4 FLOWER :------12 : :-----5 SOY :----14 : : :-------2 FLY : :--13 : :----------3 CELEGANS :-16 : : :----10 TROUT : :--15 : :-----11 FROG : : :-8 MOUSE : :--17 : : :--9 RAT : :-18 : : :--6 HOMO :--19 : :--7 PIG : :--------------1 COW branch length S.E. branch length S.E. COW 1 0.47831 0.03933 12 0.18353 0.02107 FLY 2 0.22868 0.02367 13 0.06994 0.01801 CELEGANS 3 0.34512 0.03081 14 0.12892 0.01891 FLOWER 4 0.12807 0.01598 15 0.05656 0.01291 SOY 5 0.14387 0.01671 16 0.01090 0.01170 HOMO 6 0.04715 0.00820 17 0.04886 0.00823 PIG 7 0.04347 0.00958 18 0.00377 0.00505 MOUSE 8 0.01424 0.00440 19 0.06530 0.01310 RAT 9 0.03572 0.00651 TROUT 10 0.11410 0.01525 16 iterations until convergence FROG 11 0.15038 0.01663 log L: -7560.10 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (COW:0.47831,(((FLOWER:0.12807,SOY:0.14387)100:0.18353,(FLY:0.22868, CELEGANS:0.34512)92:0.06994)100:0.12892,(TROUT:0.11410,FROG:0.15038) 79:0.05656)88:0.01090,(((MOUSE:0.01424,RAT:0.03572)96:0.04886,HOMO:0.04715) 77:0.00377,PIG:0.04347)72:0.06530); TIME STAMP Date and time: Wed Jun 04 20:22:18 2003 Runtime: 9 seconds (= 0.1 minutes = 0.0 hours)