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 313 amino acid sites Number of constant sites: 19 (= 6.1% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 7.8% pi(R) = 3.4% pi(N) = 2.9% pi(D) = 6.4% pi(C) = 0.8% pi(Q) = 1.0% pi(E) = 7.0% pi(G) = 10.0% pi(H) = 3.8% pi(I) = 8.3% pi(L) = 8.2% pi(K) = 5.5% pi(M) = 3.1% pi(F) = 3.7% pi(P) = 5.7% pi(S) = 4.4% pi(T) = 5.1% pi(W) = 1.0% pi(Y) = 3.7% pi(V) = 8.1% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.44 (S.E. 0.21) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.1306 0.1250 2 0.3128 0.1250 3 0.4930 0.1250 4 0.6915 0.1250 5 0.9257 0.1250 6 1.2249 0.1250 7 1.6610 0.1250 8 2.5603 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.69. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 8 8 8 8 8 1 8 8 8 8 8 8 8 8 8 1 8 8 1 1 8 8 8 8 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 1 8 8 8 8 1 1 8 8 6 8 8 6 1 1 8 8 8 1 3 4 3 7 7 5 1 1 2 4 4 8 6 5 7 5 8 8 5 4 3 1 1 1 3 6 7 3 1 1 8 6 7 3 7 8 4 7 7 7 8 8 7 1 2 8 1 5 1 1 1 6 1 6 1 1 4 1 4 2 8 3 4 2 5 8 5 1 7 2 8 5 3 4 6 7 4 5 6 8 6 7 4 8 8 1 8 8 8 8 6 8 5 8 6 2 2 4 1 5 5 7 8 8 6 7 6 8 4 7 5 4 7 1 8 1 2 2 5 6 8 6 5 8 8 7 6 6 3 7 4 8 2 6 1 6 3 3 8 8 7 5 8 6 3 2 2 2 1 1 1 8 5 3 8 2 1 8 7 2 3 5 1 7 7 8 5 2 2 4 2 2 2 1 1 1 5 5 6 1 1 5 8 8 5 1 8 6 3 7 4 4 3 4 1 5 8 8 3 4 1 1 1 1 3 1 7 7 5 1 8 8 1 7 4 7 1 6 3 8 2 6 8 3 6 6 8 5 5 3 4 4 2 6 4 4 3 7 8 3 6 8 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Methanobac passed 69.21% [2] Methanococ passed 57.18% [2] Archaeoglo passed 99.89% [1] Pyrococcus passed 95.72% [2] Thermotoga passed 55.12% [2] Sulfolobus passed 41.08% [2] Pyrococcu2 passed 58.67% [2] Deinococcu failed 0.00% [3] 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 4 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 Methanobac 0.00000 0.95205 1.15388 1.45399 1.57238 1.75504 2.87263 1.88428 Methanococ 0.95205 0.00000 1.13579 1.43758 1.41407 1.43289 2.34408 1.81389 Archaeoglo 1.15388 1.13579 0.00000 0.83218 1.15597 1.51273 2.02679 1.37422 Pyrococcus 1.45399 1.43758 0.83218 0.00000 1.15471 1.42234 2.21142 1.74904 Thermotoga 1.57238 1.41407 1.15597 1.15471 0.00000 1.64899 2.27006 1.59443 Sulfolobus 1.75504 1.43289 1.51273 1.42234 1.64899 0.00000 3.43396 2.12690 Pyrococcu2 2.87263 2.34408 2.02679 2.21142 2.27006 3.43396 0.00000 3.45622 Deinococcu 1.88428 1.81389 1.37422 1.74904 1.59443 2.12690 3.45622 0.00000 Average distance (over all possible pairs of sequences): 1.75688 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: 4 (= 5.7%) 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! :---Thermotoga :-54: : :---Deinococcu : :-69:-------Archaeoglo : : : :-------Pyrococcus :-88: : : : :-------Pyrococcu2 : : : :-----------Sulfolobus : :---------------Methanococ : :---------------Methanobac Quartet puzzling tree (in CLUSTAL W notation): (Methanobac,(((Thermotoga,Deinococcu)54,Archaeoglo,Pyrococcus, Pyrococcu2)69,Sulfolobus)88,Methanococ); 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) **...... : 883 **...*.. : 692 ****.**. : 540 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **..**** : 369 **.***.* : 281 ****.*.* : 260 **..**.* : 247 ****.*.. : 186 **...*.* : 132 **.*.*.. : 132 **...**. : 118 ***..**. : 87 ***..*.. : 85 ***.*.** : 84 ***.**.* : 81 **.*.*.* : 77 **..***. : 65 ***..... : 48 ***..*.* : 48 *....*.. : 46 *.***.** : 45 **.****. : 43 ****..*. : 41 (40 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. :----5 Thermotoga :---9 : :---------8 Deinococcu : :---3 Archaeoglo :--10 : :-----4 Pyrococcus : : : :---------------7 Pyrococcu2 :--11 : :--------6 Sulfolobus : :----2 Methanococ : :-----1 Methanobac branch length S.E. branch length S.E. Methanobac 1 0.55150 0.09071 9 0.19348 0.06888 Methanococ 2 0.44225 0.08309 10 0.16900 0.06335 Archaeoglo 3 0.38652 0.06919 11 0.18741 0.06842 Pyrococcus 4 0.55910 0.08635 Thermotoga 5 0.50120 0.09198 Sulfolobus 6 0.96265 0.13482 Pyrococcu2 7 1.87136 0.24457 8 iterations until convergence Deinococcu 8 1.09399 0.15911 log L: -3794.14 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Methanobac:0.55150,(((Thermotoga:0.50120,Deinococcu:1.09399)54:0.19348, Archaeoglo:0.38652,Pyrococcus:0.55910,Pyrococcu2:1.87136)69:0.16900, Sulfolobus:0.96265)88:0.18741,Methanococ:0.44225); TIME STAMP Date and time: Fri Jun 18 17:15:59 1999 Runtime: 96 seconds (= 1.6 minutes = 0.0 hours)