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: 12 sequences with 406 amino acid sites Number of constant sites: 19 (= 4.7% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 10.6% pi(R) = 5.0% pi(N) = 3.5% pi(D) = 5.0% pi(C) = 0.9% pi(Q) = 3.0% pi(E) = 8.0% pi(G) = 9.0% pi(H) = 1.6% pi(I) = 8.6% pi(L) = 9.4% pi(K) = 5.5% pi(M) = 2.4% pi(F) = 3.1% pi(P) = 3.3% pi(S) = 6.1% pi(T) = 4.2% pi(W) = 1.3% pi(Y) = 2.1% pi(V) = 7.3% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.03 (S.E. 0.08) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0749 0.1250 2 0.2299 0.1250 3 0.4060 0.1250 4 0.6147 0.1250 5 0.8736 0.1250 6 1.2177 0.1250 7 1.7368 0.1250 8 2.8464 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.97. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 8 8 8 8 1 8 8 1 1 4 8 8 1 1 8 5 8 8 8 3 8 8 6 8 6 8 5 8 7 2 1 8 4 1 4 8 3 5 6 8 8 3 1 4 8 8 8 8 3 3 4 4 3 4 5 8 5 5 1 6 2 3 2 3 5 3 6 5 6 2 3 4 7 6 5 3 3 2 5 6 3 4 8 1 4 5 2 3 3 1 1 1 1 8 8 8 6 8 7 5 7 6 1 1 4 8 3 2 7 2 1 4 7 5 4 2 3 2 2 4 1 1 2 1 4 6 4 3 7 7 7 5 8 7 8 6 4 7 2 5 2 1 6 8 1 2 4 5 7 3 7 4 1 4 1 3 7 1 1 8 8 8 6 7 8 6 6 5 6 5 8 4 6 6 2 2 4 3 2 5 1 1 1 4 5 4 1 2 1 4 3 1 1 5 5 2 3 4 1 2 7 6 7 7 8 1 8 5 8 5 6 7 4 7 7 5 8 7 6 5 4 8 2 1 3 2 2 1 1 2 1 7 1 3 2 7 5 7 2 6 7 1 8 6 8 2 4 8 3 4 1 3 4 1 8 1 1 1 2 4 3 8 2 1 8 7 2 4 8 8 8 8 6 8 8 7 6 7 7 4 8 8 2 8 3 2 1 3 3 1 2 8 2 4 8 5 4 7 8 7 8 7 8 7 7 4 2 2 1 1 1 5 3 4 2 5 2 5 1 1 2 2 3 4 2 2 8 7 8 2 7 1 6 4 7 1 5 4 4 8 7 5 4 8 5 8 2 7 5 8 4 6 8 8 7 7 5 1 3 5 3 2 5 5 4 2 3 6 3 5 7 4 2 5 5 6 7 8 6 6 8 3 8 5 6 4 6 6 8 6 2 8 8 8 8 3 8 5 8 8 3 8 1 5 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Synechocys failed 0.79% [28] Erwinia failed 2.03% [18] Rickettsia failed 1.53% [19] Sulfolobus passed 43.10% [33] Methanobac passed 32.84% [27] Halobacter failed 1.90% [29] Methanococ failed 0.01% [22] Archaeoglo passed 60.81% [25] Pyrococcus passed 75.67% [27] Bacillus passed 96.61% [44] Deinococcu failed 0.01% [43] Borrelia failed 0.00% [41] The chi-square tests compares the amino acid 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 89 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. 12 Synechocys 0.00000 1.31561 1.55487 2.25661 1.85999 1.67408 2.55927 1.91112 2.03875 2.37573 2.02225 3.10566 Erwinia 1.31561 0.00000 1.51248 2.07537 1.62984 1.59125 2.53612 1.86738 2.11855 1.90187 1.85666 2.54277 Rickettsia 1.55487 1.51248 0.00000 2.19048 2.13712 1.76589 2.53700 2.10394 1.96890 1.46464 2.51902 2.54829 Sulfolobus 2.25661 2.07537 2.19048 0.00000 1.81239 1.76994 1.80255 1.57042 1.78405 1.99564 2.30682 2.58285 Methanobac 1.85999 1.62984 2.13712 1.81239 0.00000 1.18198 1.35903 1.22780 1.29314 1.90645 2.20730 2.83984 Halobacter 1.67408 1.59125 1.76589 1.76994 1.18198 0.00000 1.73519 1.16897 1.64018 1.73687 2.24605 2.79171 Methanococ 2.55927 2.53612 2.53700 1.80255 1.35903 1.73519 0.00000 1.22338 1.69184 2.12469 2.90611 3.02246 Archaeoglo 1.91112 1.86738 2.10394 1.57042 1.22780 1.16897 1.22338 0.00000 1.60356 1.95494 2.79140 2.74084 Pyrococcus 2.03875 2.11855 1.96890 1.78405 1.29314 1.64018 1.69184 1.60356 0.00000 1.87524 2.09849 2.96153 Bacillus 2.37573 1.90187 1.46464 1.99564 1.90645 1.73687 2.12469 1.95494 1.87524 0.00000 3.10446 2.71729 Deinococcu 2.02225 1.85666 2.51902 2.30682 2.20730 2.24605 2.90611 2.79140 2.09849 3.10446 0.00000 3.81514 Borrelia 3.10566 2.54277 2.54829 2.58285 2.83984 2.79171 3.02246 2.74084 2.96153 2.71729 3.81514 0.00000 Average distance (over all possible pairs of sequences): 2.07776 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: 495 Unresolved quartets: 89 (= 18.0%) 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 not completely resolved! :---Methanococ :-66: : :---Archaeoglo : : :---Sulfolobus :-63: : :---Borrelia : :-58: :---Rickettsia : :-57: : : :---Bacillus : : : : :---Methanobac : :-54: : : :---Pyrococcus : : : :-------Halobacter : :-----------Erwinia : :-----------Deinococcu : :-----------Synechocys Quartet puzzling tree (in CLUSTAL W notation): (Synechocys,((Methanococ,Archaeoglo)66,(Sulfolobus,Borrelia)63, (Rickettsia,Bacillus)57,(Methanobac,Pyrococcus)54,Halobacter)58, Erwinia,Deinococcu); 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) ******..** ** : 658 ***.****** *. : 630 **........ *. : 577 **.******. ** : 572 ****.***.* ** : 537 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **........ .. : 493 ****.....* ** : 483 *****...** ** : 352 ***......* *. : 347 *.******** .* : 327 ***....... *. : 245 *****.*.** ** : 223 ****.*...* ** : 212 ****....** ** : 206 **..*****. *. : 190 ***......* ** : 188 ****..**** ** : 141 ***......* .. : 128 ***.*****. *. : 126 ****..**.* ** : 104 ***....... .. : 102 **.******. *. : 101 ****.*..** ** : 92 *.*....... .. : 88 *********. *. : 84 (198 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. :------7 Methanococ :---13 : :----8 Archaeoglo : : :------4 Sulfolobus :---14 : :-------------12 Borrelia :----17 : : :------3 Rickettsia : :----15 : : :------10 Bacillus : : : : :-----5 Methanobac : :--16 : : :------9 Pyrococcus : : : :------6 Halobacter : :-----2 Erwinia : :-----------11 Deinococcu : :------1 Synechocys branch length S.E. branch length S.E. Synechocys 1 0.74221 0.10624 13 0.31914 0.07476 Erwinia 2 0.69790 0.10293 14 0.35750 0.09788 Rickettsia 3 0.85064 0.12782 15 0.44793 0.10901 Sulfolobus 4 0.80052 0.11731 16 0.19038 0.06515 Methanobac 5 0.61450 0.08787 17 0.54415 0.09925 Halobacter 6 0.81068 0.09848 Methanococ 7 0.76530 0.10013 Archaeoglo 8 0.53014 0.08478 Pyrococcus 9 0.78450 0.09957 Bacillus 10 0.76877 0.14509 Deinococcu 11 1.50855 0.20672 11 iterations until convergence Borrelia 12 1.80529 0.20767 log L: -8166.58 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Synechocys:0.74221,((Methanococ:0.76530,Archaeoglo:0.53014)66:0.31914, (Sulfolobus:0.80052,Borrelia:1.80529)63:0.35750,(Rickettsia:0.85064, Bacillus:0.76877)57:0.44793,(Methanobac:0.61450,Pyrococcus:0.78450) 54:0.19038,Halobacter:0.81068)58:0.54415,Erwinia:0.69790,Deinococcu:1.50855); TIME STAMP Date and time: Fri Jun 18 17:42:53 1999 Runtime: 463 seconds (= 7.7 minutes = 0.1 hours)