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: 9 sequences with 278 amino acid sites Number of constant sites: 5 (= 1.8% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 7.4% pi(R) = 6.3% pi(N) = 4.5% pi(D) = 7.8% pi(C) = 0.5% pi(Q) = 1.7% pi(E) = 9.6% pi(G) = 4.3% pi(H) = 1.8% pi(I) = 10.6% pi(L) = 8.4% pi(K) = 8.1% pi(M) = 2.6% pi(F) = 3.9% pi(P) = 5.2% pi(S) = 2.5% pi(T) = 3.4% pi(W) = 1.3% pi(Y) = 4.8% pi(V) = 5.4% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 2.28 (S.E. 0.49) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.2341 0.1250 2 0.4337 0.1250 3 0.6053 0.1250 4 0.7802 0.1250 5 0.9757 0.1250 6 1.2145 0.1250 7 1.5487 0.1250 8 2.2078 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.44. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 1 5 4 5 5 4 1 4 1 1 1 5 1 1 1 1 1 6 2 4 1 4 2 1 5 4 1 5 4 4 8 4 2 1 1 1 5 5 1 1 1 1 4 1 1 1 5 1 4 5 6 5 1 1 5 8 3 7 8 8 8 4 1 8 2 1 3 6 3 6 8 8 3 6 8 4 1 7 3 6 3 8 8 6 2 8 8 2 3 8 7 8 8 1 1 3 1 4 2 1 3 1 1 1 1 3 1 6 5 3 8 4 6 1 3 3 2 2 6 2 1 2 1 6 3 2 4 4 1 1 8 1 2 1 7 1 7 3 5 1 8 8 4 4 2 6 3 2 8 7 1 7 8 4 1 8 7 4 5 7 4 8 8 4 3 5 6 8 5 8 8 8 8 4 7 8 8 8 8 8 5 6 8 8 8 7 8 8 2 1 3 8 8 4 2 8 8 2 1 7 8 4 3 1 8 1 3 1 4 1 8 8 3 4 7 8 3 1 1 3 7 1 1 1 4 3 1 1 8 3 3 8 8 1 1 3 8 7 3 1 4 1 3 8 8 3 3 1 4 3 1 3 8 1 1 8 1 4 1 7 7 7 8 1 4 3 3 1 1 1 3 8 1 8 1 1 1 1 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Methanococ passed 59.23% [10] Methanoco2 passed 70.77% [12] Methanoco3 passed 68.92% [19] Methanoco4 passed 73.42% [16] Methanoco5 passed 8.49% [16] Thermus failed 1.23% [23] Deinococcu failed 0.00% [18] Synechocys passed 25.67% [24] Synechocy2 failed 1.22% [18] 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 39 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. 9 Methanococ 0.00000 0.05515 0.55820 0.78499 1.19533 1.74766 2.32147 2.11957 2.02051 Methanoco2 0.05515 0.00000 0.58075 0.70823 1.30177 1.77087 2.48429 2.20454 2.22163 Methanoco3 0.55820 0.58075 0.00000 0.75572 1.22451 1.56813 1.54172 1.79218 1.63364 Methanoco4 0.78499 0.70823 0.75572 0.00000 1.41450 1.75466 2.47032 2.14009 2.20003 Methanoco5 1.19533 1.30177 1.22451 1.41450 0.00000 2.10748 2.62419 2.30333 3.25031 Thermus 1.74766 1.77087 1.56813 1.75466 2.10748 0.00000 1.69174 1.92839 1.58649 Deinococcu 2.32147 2.48429 1.54172 2.47032 2.62419 1.69174 0.00000 2.60385 2.61268 Synechocys 2.11957 2.20454 1.79218 2.14009 2.30333 1.92839 2.60385 0.00000 2.43353 Synechocy2 2.02051 2.22163 1.63364 2.20003 3.25031 1.58649 2.61268 2.43353 0.00000 Average distance (over all possible pairs of sequences): 1.76979 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: 126 Unresolved quartets: 39 (= 31.0%) 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! :---Thermus : :---Deinococcu :-80: : :---Synechocys : : :-58: :---Synechocy2 : : : :-------Methanoco3 :-98: : : : :-------Methanoco5 : : : :-----------Methanoco4 : :---------------Methanoco2 : :---------------Methanococ Quartet puzzling tree (in CLUSTAL W notation): (Methanococ,(((Thermus,Deinococcu,Synechocys,Synechocy2)80, Methanoco3,Methanoco5)58,Methanoco4)98,Methanoco2); 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) **....... : 978 *****.... : 799 **.*..... : 577 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **.**.... : 498 *****.*.* : 271 *****..** : 259 *******.. : 248 **.*.**** : 234 *****.*.. : 231 *****.**. : 196 ******.*. : 183 ***..**** : 178 *****..*. : 171 *****...* : 158 ****..... : 131 **..*.... : 108 ******..* : 107 ******... : 106 **..***** : 73 **...**** : 67 ***...... : 61 ***.*.... : 45 **.**.*.. : 40 (41 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. :-------6 Thermus : :-------------7 Deinococcu :--------10 : :------------8 Synechocys : : : :-----------9 Synechocy2 :-11 : :----3 Methanoco3 : : : :---------5 Methanoco5 :---12 : :----4 Methanoco4 : :-2 Methanoco2 : :-1 Methanococ branch length S.E. branch length S.E. Methanococ 1 0.03081 0.01991 10 0.92031 0.21429 Methanoco2 2 0.02607 0.01827 11 0.00481 0.07003 Methanoco3 3 0.37127 0.10489 12 0.27520 0.07695 Methanoco4 4 0.43677 0.09522 Methanoco5 5 1.09625 0.18632 Thermus 6 0.78747 0.19885 Deinococcu 7 1.48537 0.27401 Synechocys 8 1.44492 0.28123 9 iterations until convergence Synechocy2 9 1.25288 0.24152 log L: -2442.10 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Methanococ:0.03081,(((Thermus:0.78747,Deinococcu:1.48537,Synechocys:1.44492, Synechocy2:1.25288)80:0.92031,Methanoco3:0.37127,Methanoco5:1.09625) 58:0.00481,Methanoco4:0.43677)98:0.27520,Methanoco2:0.02607); TIME STAMP Date and time: Sat Jun 19 14:22:17 1999 Runtime: 152 seconds (= 2.5 minutes = 0.0 hours)