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 354 amino acid sites Number of constant sites: 22 (= 6.2% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 13.3% pi(R) = 7.0% pi(N) = 2.7% pi(D) = 4.4% pi(C) = 1.1% pi(Q) = 1.5% pi(E) = 3.5% pi(G) = 8.3% pi(H) = 1.5% pi(I) = 6.6% pi(L) = 13.5% pi(K) = 3.1% pi(M) = 2.2% pi(F) = 3.6% pi(P) = 5.1% pi(S) = 5.7% pi(T) = 3.8% pi(W) = 2.4% pi(Y) = 2.8% pi(V) = 7.8% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.14 (S.E. 0.11) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0924 0.1250 2 0.2581 0.1250 3 0.4368 0.1250 4 0.6427 0.1250 5 0.8935 0.1250 6 1.2219 0.1250 7 1.7112 0.1250 8 2.7435 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.88. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 1 3 8 8 8 8 8 8 8 8 8 8 6 8 5 3 7 6 2 7 7 4 2 7 6 6 1 4 1 4 8 7 8 8 7 7 8 1 1 1 4 4 6 1 4 6 1 4 7 5 5 6 8 8 6 4 7 7 8 5 3 8 8 6 5 6 5 8 1 5 6 7 8 5 6 4 5 5 5 5 5 8 6 2 6 8 4 6 8 5 7 8 8 8 7 2 6 3 3 8 6 5 8 4 7 4 5 8 4 5 7 3 6 5 1 2 8 6 5 4 5 7 2 6 7 8 5 7 5 7 3 4 6 7 4 1 6 5 3 3 4 2 1 2 1 1 2 3 4 1 6 6 4 5 3 8 2 1 2 2 1 1 3 1 1 1 3 3 1 3 3 2 2 1 2 1 5 8 8 6 8 8 8 8 8 8 5 1 8 4 1 4 3 6 4 1 2 2 4 1 1 4 1 1 1 2 1 1 4 4 5 5 4 8 8 5 1 6 4 3 1 1 4 1 1 3 7 1 6 4 2 2 1 3 2 8 3 3 5 7 7 7 4 6 8 8 7 8 4 8 6 6 7 8 1 7 7 4 7 8 3 3 8 7 7 5 3 1 1 1 3 1 7 3 3 1 2 4 1 4 2 1 4 3 5 1 3 2 3 4 8 1 8 6 6 8 7 6 4 2 5 6 7 5 7 3 6 6 4 7 8 7 6 2 3 5 4 4 4 7 5 7 3 8 4 8 7 8 8 6 7 4 8 7 8 6 8 4 8 7 8 8 5 6 8 2 5 4 8 1 1 8 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Pyrococcus failed 0.28% [5] Archaeoglo failed 0.61% [12] Rhodobacte passed 42.32% [12] Methylobac failed 0.04% [11] Pseudomona passed 57.73% [8] Methanobac passed 6.37% [11] Methanococ failed 0.00% [17] Mycobacter failed 0.04% [21] Salmonella passed 13.59% [17] Synechocys failed 4.13% [10] Deinococcu failed 0.02% [20] 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 36 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 Pyrococcus 0.00000 1.16651 2.06859 2.24560 2.30815 1.84291 1.75119 3.10057 2.86511 2.96625 3.31127 Archaeoglo 1.16651 0.00000 2.53398 2.52415 2.55503 2.05863 2.17469 3.40939 2.82719 3.08862 3.55109 Rhodobacte 2.06859 2.53398 0.00000 1.29173 1.52041 2.51780 2.71051 2.15028 2.49407 2.51681 2.55780 Methylobac 2.24560 2.52415 1.29173 0.00000 0.92065 2.56407 3.04083 2.26941 2.15066 2.54718 2.92649 Pseudomona 2.30815 2.55503 1.52041 0.92065 0.00000 2.64004 2.69931 2.30011 2.29672 2.72911 3.36026 Methanobac 1.84291 2.05863 2.51780 2.56407 2.64004 0.00000 1.80820 2.88246 2.25463 2.73338 3.26385 Methanococ 1.75119 2.17469 2.71051 3.04083 2.69931 1.80820 0.00000 3.00929 3.23723 3.33763 3.81849 Mycobacter 3.10057 3.40939 2.15028 2.26941 2.30011 2.88246 3.00929 0.00000 2.33732 2.82772 2.88843 Salmonella 2.86511 2.82719 2.49407 2.15066 2.29672 2.25463 3.23723 2.33732 0.00000 1.93604 3.35173 Synechocys 2.96625 3.08862 2.51681 2.54718 2.72911 2.73338 3.33763 2.82772 1.93604 0.00000 4.55393 Deinococcu 3.31127 3.55109 2.55780 2.92649 3.36026 3.26385 3.81849 2.88843 3.35173 4.55393 0.00000 Average distance (over all possible pairs of sequences): 2.59624 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: 36 (= 10.9%) 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 not completely resolved! :---Salmonella :-----96: : :---Synechocys : : :---Methylobac : :100: :-93:-89: :---Pseudomona : : : : : :-------Rhodobacte : : :-99: : :---Mycobacter : : :-----80: : : :---Deinococcu : : : : :---Methanobac : :---------70: : :---Methanococ : :-------------------Archaeoglo : :-------------------Pyrococcus Quartet puzzling tree (in CLUSTAL W notation): (Pyrococcus,(((Salmonella,Synechocys)96,((Methylobac,Pseudomona)100, Rhodobacte)89,(Mycobacter,Deinococcu)80)93,(Methanobac,Methanococ)70)99, Archaeoglo); 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) ***..***** * : 996 **........ . : 994 ********.. * : 956 **...**... . : 930 **...***** * : 885 *******.** . : 804 *****..*** * : 695 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **...**.** . : 443 **...***.. * : 306 **....*... . : 279 *******... . : 187 *******... * : 78 **.****.** . : 72 **...**... * : 58 **...**.** * : 54 **...***** . : 40 ***..***.. * : 23 *****.**.. * : 21 **...*.... . : 18 **...**.*. . : 17 *****..*.. * : 12 *****...** . : 11 *******..* . : 11 **.****... . : 9 ***..**... . : 8 *******.*. . : 8 ***..**.** . : 8 (28 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. :-----9 Salmonella :---12 : :-------10 Synechocys :----16 : : :---4 Methylobac : : :---13 : : : :----5 Pseudomona : :--14 : : :----3 Rhodobacte : : : : :-------8 Mycobacter : :---15 : :--------------11 Deinococcu :---18 : : :------6 Methanobac : :-17 : :------7 Methanococ : :-----2 Archaeoglo : :---1 Pyrococcus branch length S.E. branch length S.E. Pyrococcus 1 0.39950 0.08992 12 0.50910 0.13217 Archaeoglo 2 0.81755 0.11357 13 0.37081 0.08593 Rhodobacte 3 0.62948 0.10165 14 0.31729 0.09616 Methylobac 4 0.39047 0.07352 15 0.41280 0.15337 Pseudomona 5 0.53240 0.08189 16 0.66570 0.13375 Methanobac 6 0.91882 0.13770 17 0.16786 0.08936 Methanococ 7 0.98390 0.14140 18 0.37227 0.10361 Mycobacter 8 1.06807 0.17740 Salmonella 9 0.80236 0.12972 Synechocys 10 1.10127 0.15351 12 iterations until convergence Deinococcu 11 2.29508 0.33119 log L: -7146.42 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Pyrococcus:0.39950,(((Salmonella:0.80236,Synechocys:1.10127)96:0.50910, ((Methylobac:0.39047,Pseudomona:0.53240)100:0.37081,Rhodobacte:0.62948) 89:0.31729,(Mycobacter:1.06807,Deinococcu:2.29508)80:0.41280)93:0.66570, (Methanobac:0.91882,Methanococ:0.98390)70:0.16786)99:0.37227,Archaeoglo:0.81755); TIME STAMP Date and time: Fri Jun 18 21:08:58 1999 Runtime: 340 seconds (= 5.7 minutes = 0.1 hours)