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: 7 sequences with 414 amino acid sites Number of constant sites: 10 (= 2.4% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 6.2% pi(R) = 8.5% pi(N) = 2.6% pi(D) = 4.5% pi(C) = 0.6% pi(Q) = 1.6% pi(E) = 9.8% pi(G) = 5.7% pi(H) = 2.2% pi(I) = 9.9% pi(L) = 8.5% pi(K) = 6.5% pi(M) = 2.8% pi(F) = 2.9% pi(P) = 3.8% pi(S) = 6.1% pi(T) = 4.8% pi(W) = 0.7% pi(Y) = 3.7% pi(V) = 8.5% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.31 (S.E. 0.19) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.1104 0.1250 2 0.2848 0.1250 3 0.4648 0.1250 4 0.6674 0.1250 5 0.9102 0.1250 6 1.2241 0.1250 7 1.6867 0.1250 8 2.6515 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.77. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 1 8 6 7 8 7 8 3 8 4 1 5 4 6 8 8 1 1 1 3 1 3 1 2 1 1 6 1 7 3 4 5 5 6 8 8 1 4 8 8 2 8 8 5 8 8 8 2 6 2 8 8 8 8 6 5 5 4 4 3 4 7 6 8 3 4 8 8 1 8 8 3 6 5 8 5 7 2 6 3 1 8 5 4 1 8 4 2 8 8 5 8 1 5 2 2 1 2 2 2 2 1 1 2 1 1 1 3 2 1 5 1 5 1 7 2 1 2 1 5 5 4 2 5 1 1 3 1 1 1 1 2 1 5 5 2 3 4 5 3 7 1 1 4 3 7 1 3 4 5 1 6 5 4 1 4 8 7 8 8 8 4 5 5 6 8 3 8 5 8 5 7 4 1 1 6 4 2 2 8 8 1 8 6 2 5 5 3 1 1 6 1 3 5 7 2 2 8 3 4 2 1 1 1 5 1 4 1 1 3 5 3 5 7 7 8 7 7 8 7 6 7 5 7 6 5 5 6 5 8 4 2 6 8 2 5 8 2 1 7 6 1 7 4 3 8 8 3 7 2 4 7 8 4 2 5 7 2 2 7 4 1 3 8 1 3 3 4 3 7 8 8 1 4 4 6 8 2 1 5 3 4 1 5 6 4 6 8 1 4 4 6 6 6 6 8 2 4 5 8 8 7 8 8 7 8 8 7 8 8 6 8 8 5 7 7 8 3 8 5 1 1 1 1 8 8 1 1 1 8 1 1 8 5 1 5 8 8 1 1 5 3 1 1 8 1 8 1 8 8 5 1 8 1 8 1 8 1 1 1 3 8 8 1 5 1 1 1 1 8 3 8 1 3 8 6 3 1 8 8 1 1 1 1 1 1 8 1 5 8 5 8 6 3 1 8 1 3 1 8 3 8 8 1 8 3 1 8 1 8 8 8 8 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Pyrococcus passed 76.28% [3] Pyrococcu2 passed 28.69% [4] Methanothe passed 98.71% [3] Methanobac passed 99.97% [3] Methanococ passed 83.38% [3] Deinococcu failed 0.00% [5] Methanoba2 passed 8.81% [7] The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. Warning: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! The number in square brackets indicates how often each sequence is involved in one of the 7 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. 7 Pyrococcus 0.00000 0.31566 1.66532 1.81121 1.78274 1.94034 2.03824 Pyrococcu2 0.31566 0.00000 1.97284 1.80594 2.61339 2.32745 2.90558 Methanothe 1.66532 1.97284 0.00000 0.42958 1.37226 1.91390 2.08108 Methanobac 1.81121 1.80594 0.42958 0.00000 1.48880 1.86567 2.13743 Methanococ 1.78274 2.61339 1.37226 1.48880 0.00000 2.20743 2.17948 Deinococcu 1.94034 2.32745 1.91390 1.86567 2.20743 0.00000 2.38333 Methanoba2 2.03824 2.90558 2.08108 2.13743 2.17948 2.38333 0.00000 Average distance (over all possible pairs of sequences): 1.86846 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: 35 Unresolved quartets: 7 (= 20.0%) 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 completely resolved. :---Methanothe :100: :-87: :---Methanobac : : :-52: :-------Methanococ : : :100: :-----------Methanoba2 : : : :---------------Deinococcu : :-------------------Pyrococcu2 : :-------------------Pyrococcus Quartet puzzling tree (in CLUSTAL W notation): (Pyrococcus,((((Methanothe,Methanobac)100,Methanococ)87,Methanoba2)52, Deinococcu)100,Pyrococcu2); 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 **..... : 996 **...** : 871 **...*. : 515 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *****.. : 279 **....* : 205 ****.*. : 71 **..**. : 36 **..*.. : 14 ****... : 9 *.....* : 4 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--3 Methanothe :------8 : :---4 Methanobac :----9 : :--------5 Methanococ :--10 : :--------------7 Methanoba2 :-------11 : :-------------6 Deinococcu : :--2 Pyrococcu2 : :--1 Pyrococcus branch length S.E. branch length S.E. Pyrococcus 1 0.11019 0.04568 8 0.51789 0.10232 Pyrococcu2 2 0.18546 0.05331 9 0.25886 0.10263 Methanothe 3 0.14291 0.04265 10 0.15906 0.09343 Methanobac 4 0.29291 0.04968 11 0.66247 0.12833 Methanococ 5 0.77792 0.11898 Deinococcu 6 1.34436 0.19114 16 iterations until convergence Methanoba2 7 1.44213 0.21718 log L: -3889.94 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Pyrococcus:0.11019,((((Methanothe:0.14291,Methanobac:0.29291)100:0.51789, Methanococ:0.77792)87:0.25886,Methanoba2:1.44213)52:0.15906,Deinococcu:1.34436) 100:0.66247,Pyrococcu2:0.18546); TIME STAMP Date and time: Thu Jun 17 12:32:54 1999 Runtime: 123 seconds (= 2.0 minutes = 0.0 hours)