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: 13 sequences with 572 amino acid sites Number of constant sites: 14 (= 2.4% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 10.3% pi(R) = 4.7% pi(N) = 4.6% pi(D) = 6.1% pi(C) = 0.8% pi(Q) = 3.7% pi(E) = 6.6% pi(G) = 6.7% pi(H) = 2.1% pi(I) = 5.7% pi(L) = 10.0% pi(K) = 5.2% pi(M) = 2.0% pi(F) = 5.1% pi(P) = 4.6% pi(S) = 6.1% pi(T) = 5.3% pi(W) = 0.8% pi(Y) = 3.0% pi(V) = 6.6% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.17 (S.E. 0.07) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0903 0.1250 2 0.2548 0.1250 3 0.4333 0.1250 4 0.6396 0.1250 5 0.8913 0.1250 6 1.2215 0.1250 7 1.7141 0.1250 8 2.7550 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.85. 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 8 8 8 8 8 8 8 8 8 8 7 8 4 1 6 4 5 2 2 2 7 6 5 8 8 6 8 3 1 6 3 2 5 5 6 2 2 1 7 3 2 1 1 4 6 1 8 8 5 2 5 4 8 8 8 6 7 7 7 8 7 7 8 7 4 8 8 8 8 2 6 5 4 3 8 7 2 4 6 6 4 3 7 8 8 4 2 2 7 8 5 4 7 8 6 5 8 6 8 1 8 8 8 8 1 3 1 5 7 6 5 4 7 3 3 4 5 4 5 7 8 8 7 8 6 7 3 8 8 1 2 5 7 4 4 2 3 3 1 1 1 5 1 1 1 1 3 1 2 2 5 3 3 5 4 3 4 7 3 3 8 6 5 6 8 5 8 6 1 8 1 6 5 5 6 4 1 3 3 1 1 1 1 1 1 1 1 1 2 4 5 1 4 6 2 4 8 3 2 7 2 4 3 1 5 1 7 3 2 3 1 5 4 1 4 4 1 2 6 3 4 7 4 8 1 2 8 4 3 3 3 7 1 6 1 1 3 1 1 2 5 1 1 5 3 4 6 1 8 3 2 3 8 6 6 8 8 8 8 8 6 2 5 2 1 1 1 1 1 5 4 1 4 5 2 1 4 2 1 3 3 6 3 6 6 7 4 5 8 7 7 8 8 7 8 8 8 8 3 6 4 4 2 1 2 1 1 2 1 2 2 5 1 2 3 6 2 2 7 2 1 2 3 4 7 4 3 5 3 3 2 1 5 1 2 3 3 5 3 4 5 6 3 2 8 4 7 6 5 7 8 8 8 8 8 8 8 8 8 6 7 4 6 3 1 6 1 2 1 1 1 1 2 7 2 1 1 4 2 1 5 3 6 5 4 7 7 6 8 8 1 8 3 4 4 8 8 7 1 6 8 6 3 7 7 2 7 7 8 7 7 8 8 4 8 5 8 3 8 6 8 8 6 8 8 8 8 7 5 7 8 7 2 8 2 6 7 3 3 1 4 6 2 8 8 2 3 6 6 4 5 6 8 8 8 1 1 8 3 4 6 5 1 1 1 2 1 3 2 5 7 2 4 8 4 8 6 8 6 3 8 8 8 8 8 7 8 7 8 8 5 6 7 4 4 1 6 1 2 2 3 3 1 2 6 2 3 3 4 8 2 5 5 4 7 7 6 1 7 6 8 8 5 7 6 1 8 8 5 8 8 7 8 7 7 3 7 6 7 8 8 7 8 8 8 4 6 7 8 4 2 7 8 3 6 8 8 6 8 8 8 6 8 8 8 8 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Serratia passed 22.66% [9] Ecoli passed 89.04% [13] Haemophilu passed 86.90% [13] Corynebact passed 7.26% [10] Methylobac passed 79.78% [11] Deinococcu passed 42.34% [16] Pseudomona passed 17.38% [17] Schizosacc passed 35.53% [6] Eremotheci failed 0.18% [12] Saccharomy passed 5.88% [13] Helicobact failed 0.15% [35] Mycobacter failed 0.03% [8] Thermotoga passed 5.28% [5] 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 42 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. 13 Serratia 0.00000 0.21741 0.55066 2.99767 2.78494 2.24678 2.26114 2.59079 2.55762 2.35119 3.65369 5.72563 5.34371 Ecoli 0.21741 0.00000 0.56691 2.87837 2.61062 2.30023 2.36377 2.61624 2.37813 2.40121 3.69720 6.08807 6.11048 Haemophilu 0.55066 0.56691 0.00000 2.86030 2.72922 2.45921 2.49451 2.65987 2.49057 2.37085 3.65940 5.94876 5.18636 Corynebact 2.99767 2.87837 2.86030 0.00000 0.77449 0.98688 1.71557 1.94068 1.73705 1.74907 3.30646 5.40643 5.80287 Methylobac 2.78494 2.61062 2.72922 0.77449 0.00000 0.82055 1.56854 1.86759 1.62447 1.68239 2.84877 5.87623 5.40195 Deinococcu 2.24678 2.30023 2.45921 0.98688 0.82055 0.00000 1.40835 1.39076 1.38315 1.37220 2.77527 3.46861 3.66015 Pseudomona 2.26114 2.36377 2.49451 1.71557 1.56854 1.40835 0.00000 1.84196 1.84613 1.71541 3.03995 5.49121 6.33086 Schizosacc 2.59079 2.61624 2.65987 1.94068 1.86759 1.39076 1.84196 0.00000 0.88647 0.83159 2.60400 6.10063 6.64983 Eremotheci 2.55762 2.37813 2.49057 1.73705 1.62447 1.38315 1.84613 0.88647 0.00000 0.50562 2.70050 6.49119 6.39365 Saccharomy 2.35119 2.40121 2.37085 1.74907 1.68239 1.37220 1.71541 0.83159 0.50562 0.00000 2.67398 6.73495 6.34459 Helicobact 3.65369 3.69720 3.65940 3.30646 2.84877 2.77527 3.03995 2.60400 2.70050 2.67398 0.00000 7.02305 7.23070 Mycobacter 5.72563 6.08807 5.94876 5.40643 5.87623 3.46861 5.49121 6.10063 6.49119 6.73495 7.02305 0.00000 0.95314 Thermotoga 5.34371 6.11048 5.18636 5.80287 5.40195 3.66015 6.33086 6.64983 6.39365 6.34459 7.23070 0.95314 0.00000 Average distance (over all possible pairs of sequences): 3.14243 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: 715 Unresolved quartets: 42 (= 5.9%) 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! :---Eremotheci :-99: :-95: :---Saccharomy : : :-87: :-------Schizosacc : : : :-----------Helicobact : : :---Corynebact :---------81: : :---Methylobac :-96: : : :---Mycobacter : : :100: : :-----51: :---Thermotoga :-98: : : : : : :-------Deinococcu : : : : : :---------------Pseudomona : : : :-------------------Haemophilu : :-----------------------Ecoli : :-----------------------Serratia Quartet puzzling tree (in CLUSTAL W notation): (Serratia,(((((Eremotheci,Saccharomy)99,Schizosacc)95,Helicobact)87, (Corynebact,Methylobac)81,((Mycobacter,Thermotoga)100,Deinococcu)51, Pseudomona)96,Haemophilu)98,Ecoli); 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) ********** *.. : 999 ********.. *** : 990 **........ ... : 978 ***....... ... : 959 *******... *** : 952 *******... .** : 865 ***..***** *** : 807 *****.**** *.. : 508 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ***..*.... .** : 377 ***..*.*** *** : 341 ***...**** *.. : 296 ******.... .** : 292 ***...**** *** : 282 ***....... .** : 249 ***....*** *.. : 162 ***....*** *** : 149 ***...*... ... : 148 ***.**.*** *** : 118 ***..**... .** : 104 ***...*... .** : 63 ****.*.*** *** : 59 *******.** .** : 35 **....*... ... : 24 ***....*** ... : 21 ******.... *** : 21 ***....... *.. : 20 ***...*... *.. : 13 ***..*.... *** : 13 (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. :--9 Eremotheci :-14 : :-10 Saccharomy :--15 : :--8 Schizosacc :--16 : :--------11 Helicobact : : :--4 Corynebact :--17 : :--5 Methylobac :--------20 : : :---12 Mycobacter : : :---------------------18 : : : :--13 Thermotoga : :--19 : : :-6 Deinococcu : : : :----7 Pseudomona :-21 : :--3 Haemophilu : :-2 Ecoli : :-1 Serratia branch length S.E. branch length S.E. Serratia 1 0.11027 0.02464 14 0.20653 0.04804 Ecoli 2 0.13390 0.02607 15 0.37822 0.08201 Haemophilu 3 0.40037 0.05325 16 0.36505 0.08580 Corynebact 4 0.47423 0.06031 17 0.46651 0.07785 Methylobac 5 0.34753 0.05436 18 5.47958 0.75275 Deinococcu 6 0.10428 0.09026 19 0.44067 0.09738 Pseudomona 7 1.01132 0.10826 20 2.03313 0.20881 Schizosacc 8 0.44616 0.05652 21 0.12599 0.04777 Eremotheci 9 0.29228 0.03860 Saccharomy 10 0.23706 0.03641 Helicobact 11 2.14599 0.20773 Mycobacter 12 0.73737 0.10767 39 iterations until convergence Thermotoga 13 0.38105 0.10302 log L: -10742.73 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Serratia:0.11027,(((((Eremotheci:0.29228,Saccharomy:0.23706)99:0.20653, Schizosacc:0.44616)95:0.37822,Helicobact:2.14599)87:0.36505,(Corynebact:0.47423, Methylobac:0.34753)81:0.46651,((Mycobacter:0.73737,Thermotoga:0.38105) 100:5.47958,Deinococcu:0.10428)51:0.44067,Pseudomona:1.01132)96:2.03313, Haemophilu:0.40037)98:0.12599,Ecoli:0.13390); TIME STAMP Date and time: Thu Jun 17 13:29:37 1999 Runtime: 1221 seconds (= 20.4 minutes = 0.3 hours)