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: 34 sequences with 1507 amino acid sites Number of constant sites: 14 (= 0.9% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 6.3% pi(R) = 5.3% pi(N) = 4.2% pi(D) = 6.2% pi(C) = 1.4% pi(Q) = 2.9% pi(E) = 8.2% pi(G) = 5.7% pi(H) = 2.3% pi(I) = 6.2% pi(L) = 9.0% pi(K) = 7.4% pi(M) = 1.8% pi(F) = 4.5% pi(P) = 4.4% pi(S) = 5.4% pi(T) = 4.9% pi(W) = 2.4% pi(Y) = 4.2% pi(V) = 7.4% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value Pyrococcus failed 0.00% [82] Methanococ failed 0.00% [99] METHANOBAC failed 0.00% [50] Archaeoglo failed 0.00% [102] Sulfolobus passed 23.91% [146] Arabidopsi passed 28.84% [151] Tetrahymen failed 3.10% [136] Homosapien failed 3.72% [132] Celegans passed 23.63% [111] Saccharomy passed 46.46% [126] Schizosacc passed 99.80% [111] Nosema failed 0.19% [175] Chlamydia passed 78.86% [157] Chlamydoph passed 83.32% [133] Borrelia failed 0.00% [145] Treponema failed 0.00% [171] Mycobacter failed 0.00% [146] Rickettsia failed 0.02% [160] Staphyloco failed 0.00% [138] Thermus failed 0.00% [154] Helicobact failed 0.05% [184] Campylobac failed 0.08% [183] Haemophilu passed 87.24% [138] Ecoli failed 0.00% [132] Pseudomona failed 1.17% [130] Streptococ passed 28.91% [141] Bacillus passed 95.53% [128] Fervidobac passed 53.76% [131] Thermotoga failed 2.84% [182] Aquifex failed 0.41% [190] Ciona passed 6.88% [389] Synechocys failed 0.67% [120] Mycoplasma failed 0.00% [125] Deinococcu failed 0.00% [430] 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 1307 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. 34 Pyrococcus 0.00000 0.82650 0.83797 0.89302 0.94910 1.75726 1.85327 1.74888 1.76125 1.68309 1.72183 1.62609 1.62444 1.59652 1.49644 1.64214 1.54037 1.75741 1.43751 1.18206 1.99893 1.99646 1.85262 2.06623 2.00965 1.92417 1.72876 1.61218 1.69248 1.76808 1.99694 2.05394 1.91974 1.93543 Methanococ 0.82650 0.00000 0.85911 1.00647 1.00445 1.84511 1.82556 1.75320 1.75264 1.66618 1.74112 1.58566 1.68293 1.71314 1.58563 1.78505 1.77980 1.74480 1.58626 1.31069 1.96993 1.95403 1.73718 1.88188 1.92141 1.87592 1.73715 1.59416 1.64019 1.73082 1.89911 1.95529 1.90691 1.87108 METHANOBAC 0.83797 0.85911 0.00000 0.79584 0.96717 1.76096 1.78763 1.69463 1.79666 1.67357 1.66841 1.49526 1.56123 1.57282 1.50145 1.64148 1.61629 1.68327 1.51189 1.16658 1.98418 2.06993 1.75694 1.96486 1.82155 1.78722 1.60983 1.57294 1.63334 1.82259 1.99856 1.95102 1.74035 2.04272 Archaeoglo 0.89302 1.00647 0.79584 0.00000 0.92645 1.76368 1.80584 1.80021 1.83984 1.71432 1.74593 1.54715 1.62377 1.64810 1.59895 1.75406 1.71761 1.80690 1.50418 1.30447 1.95829 1.93790 1.68421 1.83541 1.82664 1.79848 1.62450 1.61501 1.60683 1.71517 1.94878 1.98014 1.98560 1.93796 Sulfolobus 0.94910 1.00445 0.96717 0.92645 0.00000 1.57440 1.43425 1.49564 1.56561 1.51343 1.57107 1.60786 1.68523 1.59856 1.47444 1.62763 1.60691 1.71063 1.36242 1.42564 1.59044 1.62586 1.32535 1.48817 1.66060 1.50741 1.41627 1.34472 1.31330 1.42109 1.76315 1.53957 1.81201 2.21132 Arabidopsi 1.75726 1.84511 1.76096 1.76368 1.57440 0.00000 0.82622 0.91491 0.93929 0.84401 0.83309 0.93571 1.06893 1.11156 1.14439 1.21164 1.26524 1.30757 1.52960 1.27792 2.28496 2.27071 2.06482 2.27591 2.11580 2.09505 1.99590 1.99116 2.03108 2.03213 2.22733 2.31224 2.09318 1.62996 Tetrahymen 1.85327 1.82556 1.78763 1.80584 1.43425 0.82622 0.00000 0.83897 0.92102 0.91222 0.86726 0.92873 1.18796 1.22325 1.14487 1.35315 1.35543 1.34877 1.50476 1.33845 2.27132 2.28403 2.16368 2.23306 2.20921 2.04114 2.06201 2.04307 2.09193 2.11774 2.17370 2.37390 2.16557 1.76102 Homosapien 1.74888 1.75320 1.69463 1.80021 1.49564 0.91491 0.83897 0.00000 0.68977 0.76977 0.72571 0.82487 1.05110 1.08427 1.11446 1.21505 1.22727 1.29788 1.52646 1.26760 2.21510 2.18679 2.11109 2.22748 2.15799 2.19254 2.10149 1.95849 1.95410 2.09208 2.20012 2.35931 2.09430 1.76616 Celegans 1.76125 1.75264 1.79666 1.83984 1.56561 0.93929 0.92102 0.68977 0.00000 0.82927 0.83411 0.82261 1.08129 1.12595 1.16485 1.26465 1.31936 1.28450 1.46446 1.30824 2.32601 2.31638 2.12185 2.24472 2.14986 2.01173 1.94276 2.04733 2.07639 2.07349 2.23945 2.29314 2.10525 1.58431 Saccharomy 1.68309 1.66618 1.67357 1.71432 1.51343 0.84401 0.91222 0.76977 0.82927 0.00000 0.56633 0.90502 1.13499 1.17379 1.11372 1.25035 1.27180 1.35951 1.43430 1.33915 2.37325 2.31727 2.17583 2.28067 2.13491 2.12193 1.99895 1.98364 2.01087 2.19724 2.22189 2.41594 2.15533 1.93808 Schizosacc 1.72183 1.74112 1.66841 1.74593 1.57107 0.83309 0.86726 0.72571 0.83411 0.56633 0.00000 0.89001 1.04375 1.05966 1.14056 1.20298 1.23667 1.32791 1.47161 1.22250 2.37770 2.27862 2.12576 2.28871 2.07306 2.13595 2.06405 2.01469 1.99308 2.21232 2.44537 2.42905 2.17997 1.76501 Nosema 1.62609 1.58566 1.49526 1.54715 1.60786 0.93571 0.92873 0.82487 0.82261 0.90502 0.89001 0.00000 0.92147 0.83732 0.94991 1.09921 1.17881 1.12397 1.33265 1.43014 1.98390 2.05723 1.95464 1.97553 2.02089 2.06903 1.92177 1.86433 1.79532 1.89850 2.35001 2.04711 2.10972 1.80481 Chlamydia 1.62444 1.68293 1.56123 1.62377 1.68523 1.06893 1.18796 1.05110 1.08129 1.13499 1.04375 0.92147 0.00000 0.40638 1.01719 1.08902 1.19800 1.25840 1.35877 1.12875 2.21119 2.21386 2.16848 2.20311 2.10982 2.11571 2.06530 1.92061 1.93548 2.07445 2.00274 2.20402 2.08894 1.57355 Chlamydoph 1.59652 1.71314 1.57282 1.64810 1.59856 1.11156 1.22325 1.08427 1.12595 1.17379 1.05966 0.83732 0.40638 0.00000 1.02039 1.11614 1.21224 1.22226 1.35288 1.14239 2.22819 2.38336 2.17521 2.25801 2.20121 2.17474 2.16871 1.97977 2.04133 2.14405 2.11061 2.33951 2.08148 1.68138 Borrelia 1.49644 1.58563 1.50145 1.59895 1.47444 1.14439 1.14487 1.11446 1.16485 1.11372 1.14056 0.94991 1.01719 1.02039 0.00000 0.86878 1.21345 1.18716 1.23609 1.12214 2.15710 2.25742 2.10132 2.29480 2.17246 2.13688 2.08216 1.89219 1.94096 1.99749 2.14517 2.28749 2.13295 1.83657 Treponema 1.64214 1.78505 1.64148 1.75406 1.62763 1.21164 1.35315 1.21505 1.26465 1.25035 1.20298 1.09921 1.08902 1.11614 0.86878 0.00000 1.14386 1.30162 1.41298 1.17309 2.31773 2.37874 2.19740 2.20740 2.15954 2.31944 2.18690 1.98026 2.04754 2.25724 2.22747 2.30069 2.25695 1.75354 Mycobacter 1.54037 1.77980 1.61629 1.71761 1.60691 1.26524 1.35543 1.22727 1.31936 1.27180 1.23667 1.17881 1.19800 1.21224 1.21345 1.14386 0.00000 0.89501 1.35075 1.10609 2.23924 2.36547 2.08094 2.18881 2.09426 2.14840 1.98195 1.98426 2.07402 2.16453 2.19352 2.19946 2.26987 1.77801 Rickettsia 1.75741 1.74480 1.68327 1.80690 1.71063 1.30757 1.34877 1.29788 1.28450 1.35951 1.32791 1.12397 1.25840 1.22226 1.18716 1.30162 0.89501 0.00000 1.37422 1.33206 2.15867 2.24483 2.18167 2.26965 2.23462 2.24593 2.13557 2.10178 2.18641 2.13671 2.18584 2.25457 2.16359 1.87296 Staphyloco 1.43751 1.58626 1.51189 1.50418 1.36242 1.52960 1.50476 1.52646 1.46446 1.43430 1.47161 1.33265 1.35877 1.35288 1.23609 1.41298 1.35075 1.37422 0.00000 0.98226 1.99878 2.09400 2.01675 2.05216 2.22723 2.02781 1.90558 1.86135 1.85088 2.01435 1.92046 2.17029 2.07088 1.50272 Thermus 1.18206 1.31069 1.16658 1.30447 1.42564 1.27792 1.33845 1.26760 1.30824 1.33915 1.22250 1.43014 1.12875 1.14239 1.12214 1.17309 1.10609 1.33206 0.98226 0.00000 1.96708 2.04073 1.83837 2.00197 1.89435 1.86057 1.76258 1.61722 1.74615 1.75985 2.11191 1.78812 2.04568 1.50655 Helicobact 1.99893 1.96993 1.98418 1.95829 1.59044 2.28496 2.27132 2.21510 2.32601 2.37325 2.37770 1.98390 2.21119 2.22819 2.15710 2.31773 2.23924 2.15867 1.99878 1.96708 0.00000 0.84254 1.28342 1.33652 1.30426 1.36281 1.26103 1.24733 1.25865 1.21635 1.53349 1.31127 1.51203 2.21202 Campylobac 1.99646 1.95403 2.06993 1.93790 1.62586 2.27071 2.28403 2.18679 2.31638 2.31727 2.27862 2.05723 2.21386 2.38336 2.25742 2.37874 2.36547 2.24483 2.09400 2.04073 0.84254 0.00000 1.18643 1.29226 1.28351 1.32955 1.22109 1.20583 1.18158 1.15720 1.44552 1.30159 1.50535 2.31615 Haemophilu 1.85262 1.73718 1.75694 1.68421 1.32535 2.06482 2.16368 2.11109 2.12185 2.17583 2.12576 1.95464 2.16848 2.17521 2.10132 2.19740 2.08094 2.18167 2.01675 1.83837 1.28342 1.18643 0.00000 0.48887 0.73118 1.11634 1.02711 1.07703 1.02375 1.01401 1.29630 1.12055 1.53297 2.30101 Ecoli 2.06623 1.88188 1.96486 1.83541 1.48817 2.27591 2.23306 2.22748 2.24472 2.28067 2.28871 1.97553 2.20311 2.25801 2.29480 2.20740 2.18881 2.26965 2.05216 2.00197 1.33652 1.29226 0.48887 0.00000 0.76661 1.17285 1.08942 1.18079 1.13161 1.11962 1.33530 1.22295 1.61135 2.19543 Pseudomona 2.00965 1.92141 1.82155 1.82664 1.66060 2.11580 2.20921 2.15799 2.14986 2.13491 2.07306 2.02089 2.10982 2.20121 2.17246 2.15954 2.09426 2.23462 2.22723 1.89435 1.30426 1.28351 0.73118 0.76661 0.00000 1.26100 1.06569 1.14661 1.15513 1.13370 1.35295 1.20468 1.37735 2.33806 Streptococ 1.92417 1.87592 1.78722 1.79848 1.50741 2.09505 2.04114 2.19254 2.01173 2.12193 2.13595 2.06903 2.11571 2.17474 2.13688 2.31944 2.14840 2.24593 2.02781 1.86057 1.36281 1.32955 1.11634 1.17285 1.26100 0.00000 0.65197 1.09647 1.06806 1.19510 1.37350 1.17868 1.32549 2.32368 Bacillus 1.72876 1.73715 1.60983 1.62450 1.41627 1.99590 2.06201 2.10149 1.94276 1.99895 2.06405 1.92177 2.06530 2.16871 2.08216 2.18690 1.98195 2.13557 1.90558 1.76258 1.26103 1.22109 1.02711 1.08942 1.06569 0.65197 0.00000 0.96208 0.89733 1.07315 1.25844 0.97786 1.24336 2.25291 Fervidobac 1.61218 1.59416 1.57294 1.61501 1.34472 1.99116 2.04307 1.95849 2.04733 1.98364 2.01469 1.86433 1.92061 1.97977 1.89219 1.98026 1.98426 2.10178 1.86135 1.61722 1.24733 1.20583 1.07703 1.18079 1.14661 1.09647 0.96208 0.00000 0.45856 0.91580 1.24813 1.04619 1.36774 2.41642 Thermotoga 1.69248 1.64019 1.63334 1.60683 1.31330 2.03108 2.09193 1.95410 2.07639 2.01087 1.99308 1.79532 1.93548 2.04133 1.94096 2.04754 2.07402 2.18641 1.85088 1.74615 1.25865 1.18158 1.02375 1.13161 1.15513 1.06806 0.89733 0.45856 0.00000 0.90434 1.25595 1.05668 1.44946 2.55182 Aquifex 1.76808 1.73082 1.82259 1.71517 1.42109 2.03213 2.11774 2.09208 2.07349 2.19724 2.21232 1.89850 2.07445 2.14405 1.99749 2.25724 2.16453 2.13671 2.01435 1.75985 1.21635 1.15720 1.01401 1.11962 1.13370 1.19510 1.07315 0.91580 0.90434 0.00000 1.30177 1.12159 1.54673 2.54998 Ciona 1.99694 1.89911 1.99856 1.94878 1.76315 2.22733 2.17370 2.20012 2.23945 2.22189 2.44537 2.35001 2.00274 2.11061 2.14517 2.22747 2.19352 2.18584 1.92046 2.11191 1.53349 1.44552 1.29630 1.33530 1.35295 1.37350 1.25844 1.24813 1.25595 1.30177 0.00000 1.03461 1.46945 2.29367 Synechocys 2.05394 1.95529 1.95102 1.98014 1.53957 2.31224 2.37390 2.35931 2.29314 2.41594 2.42905 2.04711 2.20402 2.33951 2.28749 2.30069 2.19946 2.25457 2.17029 1.78812 1.31127 1.30159 1.12055 1.22295 1.20468 1.17868 0.97786 1.04619 1.05668 1.12159 1.03461 0.00000 1.50500 2.31641 Mycoplasma 1.91974 1.90691 1.74035 1.98560 1.81201 2.09318 2.16557 2.09430 2.10525 2.15533 2.17997 2.10972 2.08894 2.08148 2.13295 2.25695 2.26987 2.16359 2.07088 2.04568 1.51203 1.50535 1.53297 1.61135 1.37735 1.32549 1.24336 1.36774 1.44946 1.54673 1.46945 1.50500 0.00000 2.30693 Deinococcu 1.93543 1.87108 2.04272 1.93796 2.21132 1.62996 1.76102 1.76616 1.58431 1.93808 1.76501 1.80481 1.57355 1.68138 1.83657 1.75354 1.77801 1.87296 1.50272 1.50655 2.21202 2.31615 2.30101 2.19543 2.33806 2.32368 2.25291 2.41642 2.55182 2.54998 2.29367 2.31641 2.30693 0.00000 Average distance (over all possible pairs of sequences): 1.67207 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: 46376 Unresolved quartets: 1307 (= 2.8%) 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! :---Fervidobac :-----90: : :---Thermotoga : : :---Streptococ :-----87: : :---Bacillus : : :---Haemophilu : :-92: :-81: :---Ecoli : : :-----------------99: :-------Pseudomona : : : : :---Helicobact : :-----80: : : :---Campylobac : : : : :---Ciona : :-----68: : : :---Synechocys : : : :-----------Aquifex : : : :-----------Mycoplasma : : :---Mycobacter :-90: :-----------------96: : : : :---Rickettsia : : : : : : :---Borrelia : : : :-------------80: : : :-98: : :---Treponema : : : : : : : : : : :---Chlamydia : : : : :-------------77: : : : : : :---Chlamydoph : : : : : : : : :-58: :---Arabidopsi : : : : :-----95: : : : : : :---Tetrahymen : : : : : : : : : :-74: :---Saccharomy : :-98: : : : :-96: :-92: : : : : : :---Schizosacc : : : : : :-72: : : : :-56: : :---Homosapien : : : : :-79: : : : : :---Celegans : : : : : : : :---------------Nosema : : : : : : :---Staphyloco : : : :-67: : : :-----------------82: :---Thermus : : : : : :-------Deinococcu : : : : :---METHANOBAC : :-----------------------------68: : : :---Archaeoglo : : : :-----------------------------------Sulfolobus : :---------------------------------------Methanococ : :---------------------------------------Pyrococcus Quartet puzzling tree (in CLUSTAL W notation): (Pyrococcus,((((Fervidobac,Thermotoga)90,(Streptococ,Bacillus)87, ((Haemophilu,Ecoli)92,Pseudomona)81,(Helicobact,Campylobac)80, (Ciona,Synechocys)68,Aquifex,Mycoplasma)99,(((Mycobacter, Rickettsia)96,((Borrelia,Treponema)80,(Chlamydia,Chlamydoph)77, (((Arabidopsi,Tetrahymen)95,((Saccharomy,Schizosacc)96,(Homosapien, Celegans)79)72)74,Nosema)56)58)98,((Staphyloco,Thermus)67, Deinococcu)82)98)90,(METHANOBAC,Archaeoglo)68,Sulfolobus)92, Methanococ); 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) ********** ********** .......... ...* : 9920 *****..... .......... ********** ***. : 9821 *****..... ........** ********** **** : 9813 *********. .********* ********** **** : 9647 ********** ******..** ********** **** : 9596 *****..*** ********** ********** **** : 9531 ********** ********** **..****** **** : 9220 **........ .......... .......... .... : 9211 *****..... .......... .......... .... : 9043 ********** ********** *******..* **** : 9004 ********** ********** *****..*** **** : 8706 ********** ********.. ********** ***. : 8207 ********** ********** **...***** **** : 8084 ********** ********** ..******** **** : 7984 ********** ****..**** ********** **** : 7965 *******..* ********** ********** **** : 7894 ********** **..****** ********** **** : 7696 *****..... .********* ********** **** : 7350 *******... .********* ********** **** : 7164 **..****** ********** ********** **** : 6841 ********** ********** ********** ..** : 6827 ********** ********.. ********** **** : 6698 *****..... ......**** ********** **** : 5793 *****..... ..******** ********** **** : 5569 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****...... .......... .......... .... : 4700 ********** ********** .......... ..** : 4677 ********** ********** *******... **** : 4563 ********** **....**** ********** **** : 4185 **...***** ********** ********** **** : 3592 ********** ********** ..*******. **** : 3591 ********** ********** ********** ...* : 3525 ********** ********.* ********** ***. : 3257 ***..***** ********** ********** **** : 3017 ********** ********** *****..*** ..** : 2865 ********** *...****** ********** **** : 2854 ********** ****....** ********** **** : 2648 *****..... ....****** ********** **** : 2565 ********** ********** .....****. **** : 2247 ********** ********** .....***** **** : 2182 ********** *.....**** ********** **** : 2125 ********** ********** ********** .*.* : 2068 ********** ********** .......... **** : 2002 ********** ********** ..*****... **** : 1902 *******... ..******** ********** **** : 1868 (663 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. :---28 Fervidobac :----35 : :---29 Thermotoga : : :-----26 Streptococ :----36 : :---27 Bacillus : : :---23 Haemophilu : :--37 : : :----24 Ecoli :----38 : :-----25 Pseudomona :---------41 : : :-----21 Helicobact : :------39 : : :-----22 Campylobac : : : : :--------31 Ciona : :----40 : : :-----32 Synechocys : : : :-------30 Aquifex : : : :------------33 Mycoplasma :---56 : : :-----17 Mycobacter : : :---42 : : : :------18 Rickettsia : : :---52 : : : : :----15 Borrelia : : : : :---43 : : : : : :------16 Treponema : : : :--51 : : : : :---13 Chlamydia : : : :-----44 : : : : :---14 Chlamydoph : : : : : : : : :-----6 Arabidopsi : : : : :--45 : : : : : :-----7 Tetrahymen : : : : :--49 : : : : : : :----10 Saccharomy : : : : : : :--46 : : : : : : : :---11 Schizosacc : : : : : :-48 : : : : : : :----8 Homosapien : : : : : :--47 : : : : : :-----9 Celegans : : : :--50 : : : :------12 Nosema : :----55 : : :-------19 Staphyloco : : :-53 : : : :-----20 Thermus : :--54 : :-------------34 Deinococcu :--58 : : :----3 METHANOBAC : :-57 : : :-----4 Archaeoglo : : : :--------5 Sulfolobus : :-----2 Methanococ : :----1 Pyrococcus branch length S.E. branch length S.E. Pyrococcus 1 0.36287 0.02714 35 0.31183 0.02714 Methanococ 2 0.46471 0.03081 36 0.33540 0.02898 METHANOBAC 3 0.36771 0.02742 37 0.14652 0.02104 Archaeoglo 4 0.46086 0.03043 38 0.36389 0.03053 Sulfolobus 5 0.67250 0.05097 39 0.50184 0.03835 Arabidopsi 6 0.45624 0.02997 40 0.32188 0.03716 Tetrahymen 7 0.44674 0.02905 41 0.82793 0.05325 Homosapien 8 0.31863 0.02430 42 0.27854 0.02877 Celegans 9 0.40611 0.02675 43 0.22330 0.02548 Saccharomy 10 0.29825 0.02290 44 0.38941 0.02933 Schizosacc 11 0.27819 0.02213 45 0.10885 0.02046 Nosema 12 0.51747 0.04059 46 0.17736 0.02011 Chlamydia 13 0.19777 0.01917 47 0.15216 0.02069 Chlamydoph 14 0.21281 0.01960 48 0.06677 0.01691 Borrelia 15 0.37055 0.02835 49 0.16276 0.02468 Treponema 16 0.51769 0.03296 50 0.18347 0.02537 Mycobacter 17 0.41513 0.03086 51 0.14756 0.02258 Rickettsia 18 0.48907 0.03297 52 0.19593 0.02660 Staphyloco 19 0.57923 0.03783 53 0.01375 0.02251 Thermus 20 0.43827 0.03493 54 0.11650 0.02494 Helicobact 21 0.45918 0.03447 55 0.31677 0.03394 Campylobac 22 0.39523 0.03248 56 0.21735 0.02991 Haemophilu 23 0.20495 0.02064 57 0.08135 0.01853 Ecoli 24 0.28985 0.02369 58 0.11165 0.01925 Pseudomona 25 0.41136 0.02985 Streptococ 26 0.40644 0.02919 Bacillus 27 0.24831 0.02354 Fervidobac 28 0.24632 0.02228 Thermotoga 29 0.22078 0.02131 Aquifex 30 0.58902 0.03597 Ciona 31 0.71078 0.06381 Synechocys 32 0.41704 0.03764 Mycoplasma 33 1.10237 0.05858 31 iterations until convergence Deinococcu 34 1.16013 0.11829 log L: -60928.65 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Pyrococcus:0.36287,((((Fervidobac:0.24632,Thermotoga:0.22078)90:0.31183, (Streptococ:0.40644,Bacillus:0.24831)87:0.33540,((Haemophilu:0.20495, Ecoli:0.28985)92:0.14652,Pseudomona:0.41136)81:0.36389,(Helicobact:0.45918, Campylobac:0.39523)80:0.50184,(Ciona:0.71078,Synechocys:0.41704) 68:0.32188,Aquifex:0.58902,Mycoplasma:1.10237)99:0.82793,(((Mycobacter:0.41513, Rickettsia:0.48907)96:0.27854,((Borrelia:0.37055,Treponema:0.51769) 80:0.22330,(Chlamydia:0.19777,Chlamydoph:0.21281)77:0.38941,(((Arabidopsi:0.45624, Tetrahymen:0.44674)95:0.10885,((Saccharomy:0.29825,Schizosacc:0.27819) 96:0.17736,(Homosapien:0.31863,Celegans:0.40611)79:0.15216)72:0.06677) 74:0.16276,Nosema:0.51747)56:0.18347)58:0.14756)98:0.19593,((Staphyloco:0.57923, Thermus:0.43827)67:0.01375,Deinococcu:1.16013)82:0.11650)98:0.31677) 90:0.21735,(METHANOBAC:0.36771,Archaeoglo:0.46086)68:0.08135,Sulfolobus:0.67250) 92:0.11165,Methanococ:0.46471); TIME STAMP Date and time: Fri Jun 18 17:52:49 1999 Runtime: 19991 seconds (= 333.2 minutes = 5.6 hours)