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: 27 sequences with 463 amino acid sites Number of constant sites: 23 (= 5.0% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 7.3% pi(R) = 5.1% pi(N) = 3.7% pi(D) = 5.7% pi(C) = 0.8% pi(Q) = 3.5% pi(E) = 7.1% pi(G) = 9.6% pi(H) = 1.6% pi(I) = 8.3% pi(L) = 9.8% pi(K) = 5.7% pi(M) = 2.1% pi(F) = 3.5% pi(P) = 4.8% pi(S) = 5.0% pi(T) = 4.5% pi(W) = 0.9% pi(Y) = 4.2% pi(V) = 7.0% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.39 (S.E. 0.08) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.1298 0.1250 2 0.3116 0.1250 3 0.4919 0.1250 4 0.6906 0.1250 5 0.9251 0.1250 6 1.2249 0.1250 7 1.6621 0.1250 8 2.5639 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.72. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 2 1 1 1 5 1 1 1 1 2 5 5 1 1 1 5 6 8 8 8 8 8 8 8 8 4 8 8 1 2 1 2 2 1 2 1 1 4 1 1 1 1 3 1 4 1 8 5 6 2 1 2 3 3 2 3 1 2 1 1 1 2 6 2 4 5 3 5 3 3 6 2 2 1 5 4 2 5 2 2 4 3 4 8 4 8 6 8 3 6 8 5 4 3 4 2 6 7 5 3 6 8 5 7 3 3 8 1 8 5 3 6 1 3 1 3 1 3 7 4 1 5 6 4 4 5 7 5 7 5 7 2 4 1 1 1 1 3 4 7 1 7 6 7 8 8 8 5 8 8 4 6 7 1 1 8 8 8 8 3 2 6 3 2 4 6 8 1 8 2 2 5 5 3 1 1 2 3 5 4 7 5 8 7 8 8 5 8 5 5 4 1 1 1 8 5 5 8 2 5 1 2 7 2 2 3 1 2 1 5 2 4 5 8 2 3 4 7 2 1 5 8 6 6 3 1 7 1 2 1 4 1 1 1 2 5 1 6 8 3 3 7 8 4 8 6 6 6 8 8 6 6 4 1 7 1 2 5 1 1 1 2 5 6 1 3 5 3 1 3 8 7 4 6 3 6 6 7 5 5 6 7 7 1 8 4 3 7 8 4 5 4 8 2 3 1 5 7 6 6 4 6 5 6 8 5 4 6 6 8 8 7 2 7 8 3 8 4 4 4 8 7 8 5 3 7 4 2 7 7 5 6 8 8 8 8 8 8 8 6 6 6 6 6 6 2 2 5 2 2 2 2 8 6 4 4 3 8 3 5 7 7 2 2 7 5 1 5 2 1 6 3 4 1 8 5 5 7 5 3 8 5 4 7 2 8 2 4 7 6 1 4 4 8 3 1 8 7 8 4 4 3 1 7 6 7 3 3 6 3 6 1 3 5 1 5 2 5 3 7 7 2 7 8 5 5 8 4 3 1 5 8 8 8 4 1 4 5 6 7 4 6 4 4 3 7 3 8 8 5 1 8 8 4 6 1 8 7 8 8 5 8 5 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Rhizobium passed 69.81% [241] Sphingomon passed 70.39% [272] Ecoli3 passed 98.69% [163] Shigella passed 85.97% [194] Salmonella passed 97.95% [215] Ecoli passed 98.61% [201] Xanthomona passed 25.35% [235] Streptococ passed 78.38% [194] Enterococc passed 86.62% [197] Methanobac passed 51.65% [290] Klebsiella passed 96.77% [119] Yersinia passed 95.09% [101] Ecoli4 passed 91.39% [267] Neisseria passed 88.06% [200] Actinobaci passed 92.24% [131] Haemophilu passed 74.94% [107] Mycobacter passed 81.10% [211] Streptomyc passed 70.30% [209] Thermotoga passed 7.43% [159] Pyrococcus passed 11.45% [235] Synechocys passed 10.66% [252] Archaeoglo passed 27.48% [281] Streptomy2 failed 0.00% [194] Methanococ failed 0.00% [192] Pyrococcu2 failed 0.00% [174] Methanoba2 failed 0.04% [114] Deinococcu passed 6.89% [236] 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 1346 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. 27 Rhizobium 0.00000 0.51739 0.56060 0.61388 0.58150 0.55093 0.61912 0.65419 0.55889 0.77639 0.61404 0.65257 0.64709 0.68748 0.69910 0.68296 0.72721 0.78699 2.31146 2.56538 2.45230 2.61305 2.80556 3.24756 3.11618 2.77986 2.32999 Sphingomon 0.51739 0.00000 0.59780 0.66375 0.59903 0.60719 0.71726 0.64671 0.68781 0.76874 0.56818 0.66852 0.65547 0.68328 0.71089 0.65117 0.82809 0.81237 2.30651 2.44379 2.51553 2.54497 2.75001 3.20671 3.72914 3.17383 2.49428 Ecoli3 0.56060 0.59780 0.00000 0.06218 0.07170 0.05954 0.55234 0.49295 0.41712 0.69268 0.49929 0.55069 0.57062 0.56366 0.51396 0.61754 0.65753 0.81973 2.14862 2.49071 2.80096 2.63349 2.67924 3.24538 3.40018 3.29446 2.36463 Shigella 0.61388 0.66375 0.06218 0.00000 0.11977 0.11543 0.59965 0.54525 0.47245 0.76868 0.58267 0.59709 0.61722 0.60225 0.56022 0.63911 0.71518 0.87767 2.18634 2.49946 2.84858 2.68697 2.68135 3.31747 3.66224 3.38734 2.50207 Salmonella 0.58150 0.59903 0.07170 0.11977 0.00000 0.08772 0.56106 0.53555 0.42384 0.69772 0.50517 0.57709 0.62115 0.58834 0.53105 0.60367 0.67597 0.83539 2.10678 2.46738 2.68237 2.63215 2.67674 3.26111 3.50942 3.20643 2.35540 Ecoli 0.55093 0.60719 0.05954 0.11543 0.08772 0.00000 0.54983 0.52785 0.43471 0.71795 0.53131 0.56986 0.60228 0.59816 0.52083 0.60379 0.66629 0.82081 2.08992 2.49682 2.69698 2.64573 2.83007 3.24137 3.39611 3.22472 2.36756 Xanthomona 0.61912 0.71726 0.55234 0.59965 0.56106 0.54983 0.00000 0.70052 0.65389 0.79509 0.67859 0.74837 0.64212 0.63467 0.57653 0.61064 0.81467 0.88201 2.36777 2.62967 2.57374 2.62715 2.70986 3.51584 3.78454 3.25982 2.53971 Streptococ 0.65419 0.64671 0.49295 0.54525 0.53555 0.52785 0.70052 0.00000 0.31788 0.58805 0.52990 0.53250 0.59052 0.50099 0.50959 0.55686 0.77939 0.80166 2.19971 2.38680 2.40574 2.49854 2.58786 2.76996 3.28780 3.07475 2.15344 Enterococc 0.55889 0.68781 0.41712 0.47245 0.42384 0.43471 0.65389 0.31788 0.00000 0.56848 0.51603 0.49380 0.52909 0.50768 0.51193 0.52253 0.65133 0.83972 2.08072 2.41334 2.46751 2.49227 2.49264 2.81495 2.99776 2.88446 2.41327 Methanobac 0.77639 0.76874 0.69268 0.76868 0.69772 0.71795 0.79509 0.58805 0.56848 0.00000 0.64771 0.59805 0.69753 0.68754 0.71453 0.61929 0.80544 0.93254 2.38331 2.86504 2.76272 2.62358 2.70981 3.44479 3.56140 3.24940 2.71070 Klebsiella 0.61404 0.56818 0.49929 0.58267 0.50517 0.53131 0.67859 0.52990 0.51603 0.64771 0.00000 0.31450 0.43540 0.46489 0.44130 0.49649 0.74906 0.88333 2.51475 2.75206 2.67396 2.97653 2.76423 3.74494 3.88662 3.59349 2.52248 Yersinia 0.65257 0.66852 0.55069 0.59709 0.57709 0.56986 0.74837 0.53250 0.49380 0.59805 0.31450 0.00000 0.39179 0.48654 0.45159 0.53869 0.84229 0.94448 2.51580 2.81332 2.74794 2.98859 2.91898 3.58454 3.83401 3.65175 2.75773 Ecoli4 0.64709 0.65547 0.57062 0.61722 0.62115 0.60228 0.64212 0.59052 0.52909 0.69753 0.43540 0.39179 0.00000 0.39585 0.38844 0.44463 0.78099 0.90083 2.44172 2.44956 2.59492 2.69881 2.72179 3.35433 3.52262 3.39447 2.48275 Neisseria 0.68748 0.68328 0.56366 0.60225 0.58834 0.59816 0.63467 0.50099 0.50768 0.68754 0.46489 0.48654 0.39585 0.00000 0.28885 0.37465 0.82191 0.97637 2.44055 2.61812 2.58341 2.78301 2.54853 3.35441 3.52573 3.35553 2.53485 Actinobaci 0.69910 0.71089 0.51396 0.56022 0.53105 0.52083 0.57653 0.50959 0.51193 0.71453 0.44130 0.45159 0.38844 0.28885 0.00000 0.40334 0.78142 0.92688 2.43873 2.62681 2.57465 2.86126 2.89659 3.49883 3.65169 3.23585 2.67546 Haemophilu 0.68296 0.65117 0.61754 0.63911 0.60367 0.60379 0.61064 0.55686 0.52253 0.61929 0.49649 0.53869 0.44463 0.37465 0.40334 0.00000 0.72207 0.75207 1.87190 2.18268 2.00191 2.07831 1.95379 3.07612 3.04943 2.72330 2.40720 Mycobacter 0.72721 0.82809 0.65753 0.71518 0.67597 0.66629 0.81467 0.77939 0.65133 0.80544 0.74906 0.84229 0.78099 0.82191 0.78142 0.72207 0.00000 0.91580 2.41666 2.56468 2.49885 2.73939 2.44125 3.43622 3.50979 2.91307 2.32940 Streptomyc 0.78699 0.81237 0.81973 0.87767 0.83539 0.82081 0.88201 0.80166 0.83972 0.93254 0.88333 0.94448 0.90083 0.97637 0.92688 0.75207 0.91580 0.00000 2.17907 2.71234 2.56000 2.72080 2.73816 3.65461 3.62170 2.96857 2.31969 Thermotoga 2.31146 2.30651 2.14862 2.18634 2.10678 2.08992 2.36777 2.19971 2.08072 2.38331 2.51475 2.51580 2.44172 2.44055 2.43873 1.87190 2.41666 2.17907 0.00000 0.87796 1.03263 1.20372 1.43756 1.97309 2.23422 2.03472 1.33461 Pyrococcus 2.56538 2.44379 2.49071 2.49946 2.46738 2.49682 2.62967 2.38680 2.41334 2.86504 2.75206 2.81332 2.44956 2.61812 2.62681 2.18268 2.56468 2.71234 0.87796 0.00000 1.05819 1.03723 1.23330 1.84724 2.16189 2.18825 1.19875 Synechocys 2.45230 2.51553 2.80096 2.84858 2.68237 2.69698 2.57374 2.40574 2.46751 2.76272 2.67396 2.74794 2.59492 2.58341 2.57465 2.00191 2.49885 2.56000 1.03263 1.05819 0.00000 1.19874 1.26823 2.25455 2.30596 2.06478 1.34729 Archaeoglo 2.61305 2.54497 2.63349 2.68697 2.63215 2.64573 2.62715 2.49854 2.49227 2.62358 2.97653 2.98859 2.69881 2.78301 2.86126 2.07831 2.73939 2.72080 1.20372 1.03723 1.19874 0.00000 1.40177 2.22428 2.19656 2.00886 1.46118 Streptomy2 2.80556 2.75001 2.67924 2.68135 2.67674 2.83007 2.70986 2.58786 2.49264 2.70981 2.76423 2.91898 2.72179 2.54853 2.89659 1.95379 2.44125 2.73816 1.43756 1.23330 1.26823 1.40177 0.00000 2.74502 2.87507 2.41276 1.28168 Methanococ 3.24756 3.20671 3.24538 3.31747 3.26111 3.24137 3.51584 2.76996 2.81495 3.44479 3.74494 3.58454 3.35433 3.35441 3.49883 3.07612 3.43622 3.65461 1.97309 1.84724 2.25455 2.22428 2.74502 0.00000 1.16069 1.34546 1.70025 Pyrococcu2 3.11618 3.72914 3.40018 3.66224 3.50942 3.39611 3.78454 3.28780 2.99776 3.56140 3.88662 3.83401 3.52262 3.52573 3.65169 3.04943 3.50979 3.62170 2.23422 2.16189 2.30596 2.19656 2.87507 1.16069 0.00000 1.20547 2.11297 Methanoba2 2.77986 3.17383 3.29446 3.38734 3.20643 3.22472 3.25982 3.07475 2.88446 3.24940 3.59349 3.65175 3.39447 3.35553 3.23585 2.72330 2.91307 2.96857 2.03472 2.18825 2.06478 2.00886 2.41276 1.34546 1.20547 0.00000 1.76012 Deinococcu 2.32999 2.49428 2.36463 2.50207 2.35540 2.36756 2.53971 2.15344 2.41327 2.71070 2.52248 2.75773 2.48275 2.53485 2.67546 2.40720 2.32940 2.31969 1.33461 1.19875 1.34729 1.46118 1.28168 1.70025 2.11297 1.76012 0.00000 Average distance (over all possible pairs of sequences): 1.73089 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: 10000 Analysed quartets: 17550 Unresolved quartets: 1346 (= 7.7%) 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! :---Streptococ :-------------91: : :---Enterococc : : :---Ecoli3 : :-86: : : :---Shigella :---------76: : :-------Salmonella : : : :-------Ecoli : : :---Neisseria :-------------65: : :---Actinobaci : : :---Methanococ : :-73: : :-66: :---Pyrococcu2 : : : : :-80: :-------Methanoba2 : : : : : :-----------Deinococcu : : :-82:-61: :---Synechocys : : : :-62: : : : : :---Streptomy2 : : : : : : :-----51: :---Pyrococcus : : :-58: : : : :---Archaeoglo : : : : : :-------Thermotoga : : : : :---Klebsiella : :-------------56: : : :---Yersinia : : : : :---Mycobacter : :-------------55: : : :---Streptomyc : : : :-------------------Xanthomona : : : :-------------------Methanobac : : : :-------------------Ecoli4 : : : :-------------------Haemophilu : :-----------------------Sphingomon : :-----------------------Rhizobium Quartet puzzling tree (in CLUSTAL W notation): (Rhizobium,((Streptococ,Enterococc)91,((Ecoli3,Shigella)86, Salmonella,Ecoli)76,(Neisseria,Actinobaci)65,((((Methanococ, Pyrococcu2)73,Methanoba2)66,Deinococcu)80,((Synechocys,Streptomy2)62, (Pyrococcus,Archaeoglo)58,Thermotoga)51)61,(Klebsiella,Yersinia)56, (Mycobacter,Streptomyc)55,Xanthomona,Methanobac,Ecoli4,Haemophilu)82, Sphingomon); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 10000 puzzling steps: Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *******..* ********** ******* : 9128 **..****** ********** ******* : 8562 **........ .......... ....... : 8224 ********** ********** ***.... : 8013 **....**** ********** ******* : 7592 ********** ********** ***..** : 7304 ********** ********** ***...* : 6577 ********** ***..***** ******* : 6527 ********** ********** .*.**** : 6150 ********** ********.. ....... : 6066 ********** *********. *.***** : 5816 ********** ..******** ******* : 5594 ********** ******..** ******* : 5525 ********** ********.. ...**** : 5079 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****..**** ********** ******* : 4516 ********** *****.**.. ....... : 4462 **.....*** ********** ******* : 4074 ********** *********. ...**** : 3595 *******... ********** ******* : 3023 *********. ..******** ******* : 2897 ********** ...******* ******* : 2795 **..*.**** ********** ******* : 2761 ********** **...***** ******* : 2740 ********** ********.. *.***** : 2685 ********** ********.. ******* : 2620 **........ ......**.. ....... : 2594 *********. *.******** ******* : 2386 ********** .....***** ******* : 2385 ********** ********** ***.**. : 2374 *********. .....***** ******* : 2299 ********** ********** ***..*. : 2274 **...***** ********** ******* : 2120 ********** *****..... ....... : 2011 *********. ...******* ******* : 1963 (1982 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. :--8 Streptococ :--28 : :-9 Enterococc : : :-3 Ecoli3 : :-29 : : :-4 Shigella :---30 : :-5 Salmonella : : : :-6 Ecoli : : :--14 Neisseria :--31 : :-15 Actinobaci : : :-----24 Methanococ : :--32 : : :----25 Pyrococcu2 : :------33 : : :----26 Methanoba2 : :--34 : : :-----27 Deinococcu :---------------38 : : :----21 Synechocys : : :--35 : : : :------23 Streptomy2 : :--37 : : :---20 Pyrococcus : :-36 : : :-----22 Archaeoglo : : : :----19 Thermotoga : : :--11 Klebsiella :-39 : :--12 Yersinia :--41 : : :----17 Mycobacter : :--40 : : :----18 Streptomyc : : : :----7 Xanthomona : : : :----10 Methanobac : : : :---13 Ecoli4 : : : :---16 Haemophilu : :---2 Sphingomon : :--1 Rhizobium branch length S.E. branch length S.E. Rhizobium 1 0.25803 0.04476 28 0.19648 0.03709 Sphingomon 2 0.31163 0.04858 29 0.02299 0.01056 Ecoli3 3 0.00473 0.00513 30 0.31901 0.04478 Shigella 4 0.05746 0.01491 31 0.16490 0.03258 Salmonella 5 0.05482 0.01549 32 0.15450 0.05463 Ecoli 6 0.04376 0.01386 33 0.73379 0.12281 Xanthomona 7 0.48769 0.05897 34 0.27264 0.08303 Streptococ 8 0.20306 0.03541 35 0.14591 0.05228 Enterococc 9 0.13027 0.02955 36 0.10139 0.04029 Methanobac 10 0.53362 0.06356 37 0.16821 0.07534 Klebsiella 11 0.17356 0.03290 38 2.10998 0.23850 Yersinia 12 0.17279 0.03276 39 0.13409 0.03121 Ecoli4 13 0.32829 0.04512 40 0.20053 0.04960 Neisseria 14 0.18138 0.03171 41 0.23153 0.04444 Actinobaci 15 0.12038 0.02662 Haemophilu 16 0.40667 0.05865 Mycobacter 17 0.47712 0.06691 Streptomyc 18 0.53910 0.07169 Thermotoga 19 0.52694 0.06724 Pyrococcus 20 0.37905 0.05699 Synechocys 21 0.49024 0.06838 Archaeoglo 22 0.68906 0.07909 Streptomy2 23 0.86454 0.09537 Methanococ 24 0.58950 0.07407 Pyrococcu2 25 0.53345 0.06998 Methanoba2 26 0.56095 0.07534 14 iterations until convergence Deinococcu 27 0.58726 0.10592 log L: -12377.00 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Rhizobium:0.25803,((Streptococ:0.20306,Enterococc:0.13027)91:0.19648, ((Ecoli3:0.00473,Shigella:0.05746)86:0.02299,Salmonella:0.05482, Ecoli:0.04376)76:0.31901,(Neisseria:0.18138,Actinobaci:0.12038) 65:0.16490,((((Methanococ:0.58950,Pyrococcu2:0.53345)73:0.15450, Methanoba2:0.56095)66:0.73379,Deinococcu:0.58726)80:0.27264,((Synechocys:0.49024, Streptomy2:0.86454)62:0.14591,(Pyrococcus:0.37905,Archaeoglo:0.68906) 58:0.10139,Thermotoga:0.52694)51:0.16821)61:2.10998,(Klebsiella:0.17356, Yersinia:0.17279)56:0.13409,(Mycobacter:0.47712,Streptomyc:0.53910) 55:0.20053,Xanthomona:0.48769,Methanobac:0.53362,Ecoli4:0.32829, Haemophilu:0.40667)82:0.23153,Sphingomon:0.31163); TIME STAMP Date and time: Sat Jun 19 15:07:20 1999 Runtime: 15710 seconds (= 261.8 minutes = 4.4 hours)