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: 8 sequences with 405 amino acid sites Number of constant sites: 9 (= 2.2% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 8.6% pi(R) = 6.4% pi(N) = 3.0% pi(D) = 5.8% pi(C) = 0.2% pi(Q) = 1.9% pi(E) = 9.6% pi(G) = 6.2% pi(H) = 0.4% pi(I) = 6.9% pi(L) = 13.2% pi(K) = 6.6% pi(M) = 2.4% pi(F) = 3.2% pi(P) = 3.4% pi(S) = 5.6% pi(T) = 4.5% pi(W) = 0.9% pi(Y) = 4.4% pi(V) = 6.7% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 2.20 (S.E. 0.29) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.2260 0.1250 2 0.4252 0.1250 3 0.5978 0.1250 4 0.7747 0.1250 5 0.9729 0.1250 6 1.2158 0.1250 7 1.5566 0.1250 8 2.2308 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.45. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 1 1 2 7 1 8 1 4 8 8 8 8 8 8 7 6 5 1 8 4 8 8 8 8 8 8 8 6 3 8 8 8 6 8 7 4 4 8 8 8 3 4 8 8 2 8 7 8 5 8 6 6 5 4 4 2 1 7 1 1 1 1 1 1 2 4 2 4 1 2 8 6 6 8 4 5 2 2 4 4 2 4 5 8 2 6 5 5 8 6 7 2 5 2 8 1 1 6 8 5 3 5 5 3 7 8 3 6 6 1 8 8 7 4 1 2 1 1 4 8 2 1 1 6 7 7 7 7 4 8 6 3 4 5 3 6 6 4 8 6 2 7 8 6 1 5 3 7 1 3 4 1 1 2 2 3 2 1 1 2 8 3 2 3 2 7 1 4 2 8 8 8 2 2 2 8 1 5 7 8 8 8 8 7 7 8 2 6 4 5 8 6 3 2 1 1 1 8 5 8 1 1 7 2 1 5 3 8 7 8 1 5 6 8 7 6 8 1 3 5 1 8 6 2 8 8 5 1 6 5 1 2 2 8 4 3 7 8 2 7 4 5 5 8 5 6 7 7 8 4 8 6 3 4 5 5 3 4 6 5 2 1 1 5 7 1 6 5 3 3 3 2 6 2 5 5 2 1 4 6 5 1 4 2 3 8 7 6 2 7 3 1 8 8 4 7 8 8 5 1 6 7 1 2 8 5 7 8 5 8 7 2 4 3 6 1 4 2 1 8 3 4 5 8 1 2 5 1 7 8 6 8 8 8 1 7 1 3 8 4 5 1 6 4 1 7 7 8 8 2 6 8 6 5 8 6 2 8 8 8 1 2 2 1 5 2 3 2 7 3 2 7 8 1 2 8 1 1 7 1 1 1 4 2 3 2 4 4 8 8 4 4 8 4 1 8 1 7 8 4 4 2 5 4 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Methanococ failed 1.52% [0] Methanobac passed 92.56% [2] Pyrococcus passed 30.67% [3] Haloferax failed 0.90% [1] Methanosar passed 27.42% [2] Archaeoglo failed 2.03% [2] Thermus failed 0.00% [0] Deinococcu failed 0.00% [2] 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 3 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. 8 Methanococ 0.00000 1.32474 1.92934 2.74964 2.87831 2.78859 3.09105 3.42116 Methanobac 1.32474 0.00000 2.26025 2.52175 2.86193 2.77291 2.90805 3.08249 Pyrococcus 1.92934 2.26025 0.00000 3.12034 2.85740 2.90833 3.19875 3.56428 Haloferax 2.74964 2.52175 3.12034 0.00000 1.93634 2.10352 2.95175 3.31943 Methanosar 2.87831 2.86193 2.85740 1.93634 0.00000 1.83940 3.18369 3.87872 Archaeoglo 2.78859 2.77291 2.90833 2.10352 1.83940 0.00000 3.29287 3.76900 Thermus 3.09105 2.90805 3.19875 2.95175 3.18369 3.29287 0.00000 2.46490 Deinococcu 3.42116 3.08249 3.56428 3.31943 3.87872 3.76900 2.46490 0.00000 Average distance (over all possible pairs of sequences): 2.82068 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: 70 Unresolved quartets: 3 (= 4.3%) 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. :---Methanosar :-93: :100: :---Archaeoglo : : :-94: :-------Haloferax : : : : :---Thermus :-98: :----100: : : :---Deinococcu : : : :---------------Pyrococcus : :-------------------Methanobac : :-------------------Methanococ Quartet puzzling tree (in CLUSTAL W notation): (Methanococ,((((Methanosar,Archaeoglo)93,Haloferax)100,(Thermus, Deinococcu)100)94,Pyrococcus)98,Methanobac); 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 ******.. : 1000 **...... : 979 ***..... : 938 ****..** : 930 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ***..*** : 56 **.***.. : 37 **....** : 25 *.*..... : 21 ***.*.** : 14 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-------5 Methanosar :---9 : :-------6 Archaeoglo :----10 : :--------4 Haloferax :---12 : : :---------7 Thermus : :------11 : :-----------8 Deinococcu :--13 : :---------3 Pyrococcus : :------2 Methanobac : :-----1 Methanococ branch length S.E. branch length S.E. Methanococ 1 0.60297 0.08968 9 0.17929 0.09052 Methanobac 2 0.73637 0.09524 10 0.45538 0.12447 Pyrococcus 3 1.19063 0.14427 11 0.81833 0.19123 Haloferax 4 1.01875 0.13509 12 0.38212 0.12406 Methanosar 5 0.87386 0.12097 13 0.28611 0.09777 Archaeoglo 6 0.94692 0.12622 Thermus 7 1.22204 0.20144 9 iterations until convergence Deinococcu 8 1.46054 0.25172 log L: -6491.66 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Methanococ:0.60297,((((Methanosar:0.87386,Archaeoglo:0.94692)93:0.17929, Haloferax:1.01875)100:0.45538,(Thermus:1.22204,Deinococcu:1.46054) 100:0.81833)94:0.38212,Pyrococcus:1.19063)98:0.28611,Methanobac:0.73637); TIME STAMP Date and time: Sat Jun 19 14:26:42 1999 Runtime: 197 seconds (= 3.3 minutes = 0.1 hours)