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 1094 amino acid sites Number of constant sites: 8 (= 0.7% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 6.4% pi(R) = 4.4% pi(N) = 4.7% pi(D) = 5.1% pi(C) = 1.2% pi(Q) = 3.9% pi(E) = 7.2% pi(G) = 5.8% pi(H) = 3.0% pi(I) = 5.8% pi(L) = 11.5% pi(K) = 6.5% pi(M) = 1.8% pi(F) = 5.2% pi(P) = 4.6% pi(S) = 7.6% pi(T) = 5.6% pi(W) = 0.7% pi(Y) = 3.6% pi(V) = 5.3% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.81 (S.E. 0.15) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.1795 0.1250 2 0.3736 0.1250 3 0.5513 0.1250 4 0.7389 0.1250 5 0.9539 0.1250 6 1.2222 0.1250 7 1.6048 0.1250 8 2.3758 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.55. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 1 8 8 8 7 4 8 7 6 8 8 8 6 3 8 8 8 7 2 5 8 8 8 8 8 1 8 1 8 1 7 8 1 1 7 8 8 1 7 6 5 3 4 6 8 2 5 1 8 2 8 8 8 8 8 1 2 1 3 8 2 6 6 6 7 6 6 1 7 7 1 4 2 8 7 5 2 4 6 2 5 1 8 1 1 3 1 2 2 7 1 4 1 7 3 8 4 1 2 1 1 1 1 1 1 1 1 1 3 1 1 1 1 7 3 1 1 3 1 1 1 1 1 5 1 4 2 3 1 1 2 1 1 2 1 1 4 1 5 3 1 6 1 6 1 1 1 2 1 8 1 3 6 1 3 6 1 1 4 2 1 1 3 1 1 1 1 6 1 4 1 4 5 8 2 1 8 1 1 1 4 1 5 1 5 8 4 8 3 5 6 6 2 6 2 5 5 4 1 1 1 3 1 1 1 1 1 2 7 3 2 7 5 7 5 3 6 7 8 6 2 4 4 6 4 4 5 8 3 1 5 6 3 1 1 1 6 1 7 8 1 6 7 1 4 5 2 8 2 8 6 1 2 5 3 3 1 4 3 2 1 2 4 7 4 5 2 1 1 4 5 5 7 5 5 4 6 6 6 3 5 6 8 5 5 8 5 8 3 8 4 6 8 7 7 8 8 2 8 7 8 7 8 5 7 6 7 5 3 8 6 8 8 5 2 8 3 8 8 8 8 3 8 5 3 5 6 7 3 5 2 6 3 7 7 4 5 8 3 5 4 5 4 3 6 2 7 2 1 6 8 2 1 4 3 4 8 2 2 1 4 3 5 5 1 2 2 1 1 2 1 8 4 4 4 8 7 2 1 7 6 8 2 3 4 4 6 7 3 4 2 1 4 4 1 3 3 7 8 6 6 5 7 5 4 6 3 1 6 4 2 2 6 5 3 4 8 5 4 8 8 1 5 8 6 7 2 1 2 4 2 2 2 5 1 3 2 8 1 2 4 5 4 7 4 8 5 2 2 2 8 1 3 7 2 7 8 8 7 3 7 2 2 6 4 1 8 5 7 1 3 6 7 8 8 3 8 8 3 1 7 8 4 6 8 2 7 8 6 4 3 2 6 1 1 4 3 2 3 4 7 1 4 1 6 4 4 4 3 5 8 1 2 8 6 5 8 4 5 7 5 3 6 3 6 5 7 1 7 6 7 8 8 8 2 5 5 1 8 5 3 8 8 6 3 8 6 8 8 8 8 1 7 8 8 1 3 6 7 3 2 8 5 8 4 2 7 1 1 8 3 4 4 4 3 2 1 8 5 7 7 4 8 8 6 8 8 8 8 8 4 8 1 6 7 2 3 8 5 8 8 8 1 1 2 2 5 2 5 4 8 8 8 7 4 3 1 8 2 2 8 2 2 8 3 3 1 2 1 4 7 8 7 3 7 4 1 1 2 7 8 6 2 4 7 4 6 6 6 3 1 7 8 6 1 1 2 3 2 4 2 8 8 5 7 7 2 5 7 8 1 8 8 8 8 8 7 7 1 1 8 8 7 7 8 5 8 7 6 3 6 6 6 7 3 1 5 6 5 1 4 5 4 6 8 8 6 8 6 6 8 5 5 7 4 8 3 4 3 1 8 2 1 8 6 2 3 2 3 3 5 5 7 7 5 3 7 5 3 2 5 3 5 4 3 2 1 8 5 1 6 6 8 2 6 4 8 8 3 8 5 5 8 5 8 1 8 8 5 1 4 6 3 3 4 7 5 4 5 3 8 8 7 8 8 5 8 8 7 8 8 7 8 5 8 6 6 5 8 8 4 4 4 8 5 8 8 7 7 8 7 7 8 8 4 4 5 4 8 2 8 6 4 8 7 8 4 3 5 8 6 8 7 1 6 7 3 3 6 5 7 1 1 1 7 7 8 8 8 8 8 8 8 8 8 8 8 4 4 7 3 6 8 6 6 5 8 8 3 4 8 8 8 7 4 5 5 8 8 8 3 1 8 4 8 1 1 7 7 2 5 6 6 6 6 4 4 6 4 8 3 4 8 4 4 8 8 4 3 3 3 3 4 2 7 2 7 4 5 3 5 2 6 6 1 4 6 4 8 1 1 6 2 1 1 2 3 1 1 1 1 1 2 3 2 3 6 3 7 8 5 1 3 1 1 4 5 1 1 1 1 1 3 7 6 6 1 5 4 5 3 8 2 3 5 7 8 6 8 2 1 8 2 7 8 3 4 5 4 4 8 6 2 3 6 4 6 8 1 2 3 6 6 8 4 2 8 2 8 3 2 7 6 4 4 6 8 4 3 7 2 8 8 5 2 8 4 3 8 5 1 1 1 7 1 5 5 5 3 8 2 2 8 8 6 3 8 8 2 5 7 5 6 1 8 8 8 8 1 8 2 8 8 3 4 8 8 7 2 7 5 5 5 4 7 8 8 8 8 8 8 8 8 8 7 7 5 8 4 6 8 6 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Chlamydoph passed 77.09% [5] Chlamydia failed 0.40% [5] Schizosacc passed 65.17% [4] Homosapien failed 0.38% [4] Saccharomy passed 11.04% [4] Deinococcu failed 0.00% [11] Treponema failed 0.00% [7] Borrelia failed 0.00% [4] 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 11 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 Chlamydoph 0.00000 0.48229 2.80747 2.58666 2.81643 2.98530 2.91898 3.19350 Chlamydia 0.48229 0.00000 2.82563 2.66086 2.81760 3.20647 2.99843 3.12324 Schizosacc 2.80747 2.82563 0.00000 1.56444 1.58766 3.03082 2.93344 3.05841 Homosapien 2.58666 2.66086 1.56444 0.00000 1.71773 2.88282 2.94925 3.33010 Saccharomy 2.81643 2.81760 1.58766 1.71773 0.00000 3.32526 3.22611 2.92368 Deinococcu 2.98530 3.20647 3.03082 2.88282 3.32526 0.00000 3.06049 3.61077 Treponema 2.91898 2.99843 2.93344 2.94925 3.22611 3.06049 0.00000 2.82809 Borrelia 3.19350 3.12324 3.05841 3.33010 2.92368 3.61077 2.82809 0.00000 Average distance (over all possible pairs of sequences): 2.76614 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: 11 (= 15.7%) 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! :---Schizosacc :-88: :100: :---Saccharomy : : : :-------Homosapien : :-98: :---Treponema : :-----91: : : :---Borrelia : : : :-----------Deinococcu : :---------------Chlamydia : :---------------Chlamydoph Quartet puzzling tree (in CLUSTAL W notation): (Chlamydoph,(((Schizosacc,Saccharomy)88,Homosapien)100,(Treponema, Borrelia)91,Deinococcu)98,Chlamydia); 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 **...... : 980 ******.. : 914 **.*.*** : 878 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **....** : 454 **...*.. : 310 *****... : 229 **..**** : 104 *****..* : 57 *....*.. : 20 ***..*** : 18 **...**. : 13 **.....* : 12 **....*. : 8 *****.*. : 3 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :------3 Schizosacc :---9 : :-------5 Saccharomy :-----10 : :------4 Homosapien :---------12 : : :----------7 Treponema : :---11 : : :------------8 Borrelia : : : :-------------6 Deinococcu : :---2 Chlamydia : :--1 Chlamydoph branch length S.E. branch length S.E. Chlamydoph 1 0.18619 0.02740 9 0.20174 0.04966 Chlamydia 2 0.29947 0.02873 10 0.61619 0.08359 Schizosacc 3 0.74284 0.06548 11 0.39593 0.08645 Homosapien 4 0.68360 0.06280 12 1.17867 0.10085 Saccharomy 5 0.85067 0.06680 Deinococcu 6 1.66262 0.23127 Treponema 7 1.30573 0.11194 16 iterations until convergence Borrelia 8 1.53847 0.12455 log L: -16367.61 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Chlamydoph:0.18619,(((Schizosacc:0.74284,Saccharomy:0.85067)88:0.20174, Homosapien:0.68360)100:0.61619,(Treponema:1.30573,Borrelia:1.53847) 91:0.39593,Deinococcu:1.66262)98:1.17867,Chlamydia:0.29947); TIME STAMP Date and time: Thu Jun 17 14:20:02 1999 Runtime: 357 seconds (= 6.0 minutes = 0.1 hours)