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: 42 sequences with 812 amino acid sites Number of constant sites: 6 (= 0.7% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 6.9% pi(R) = 6.5% pi(N) = 3.5% pi(D) = 6.2% pi(C) = 1.0% pi(Q) = 3.8% pi(E) = 8.8% pi(G) = 6.4% pi(H) = 2.2% pi(I) = 6.1% pi(L) = 9.6% pi(K) = 6.4% pi(M) = 2.5% pi(F) = 5.3% pi(P) = 4.8% pi(S) = 5.0% pi(T) = 4.5% pi(W) = 0.9% pi(Y) = 3.1% pi(V) = 6.6% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value Mycoplasma passed 17.43% [787] Mycoplasm2 failed 0.00% [775] Aquifex failed 1.49% [870] Thermotoga failed 4.21% [972] Bacillus2 passed 50.79% [746] Synechocys passed 65.45% [1047] Haemophilu failed 4.21% [804] Ecoli passed 12.82% [806] Buchnera failed 0.00% [1076] Helicobact passed 66.78% [994] Treponema failed 0.31% [1142] Borrelia failed 0.00% [1259] Thermus2 failed 0.00% [946] Mycobacter failed 0.00% [1133] Chlamydoph passed 85.72% [1031] Chlamydia passed 53.65% [973] Rickettsia passed 32.46% [1147] Mycoplasm3 failed 0.00% [1269] Lactobacil passed 40.23% [741] Thermus failed 0.00% [748] Bacillus passed 51.38% [847] Pyrococcus failed 0.52% [651] Brugia passed 35.25% [889] Celegans passed 23.46% [739] Homosapien passed 6.53% [770] Saccharomy passed 25.34% [690] Schizosacc passed 27.41% [852] Homosapie2 passed 46.79% [669] Rattusnorv passed 66.77% [644] Drosophila passed 49.58% [726] Celegans2 passed 58.38% [611] Saccharom2 passed 80.31% [649] Schizosac2 passed 42.68% [591] Arabidopsi failed 1.04% [777] Methanococ passed 71.84% [767] Methanobac passed 60.79% [988] Archaeoglo passed 11.44% [739] Pyrococcu2 passed 20.19% [847] Haloferax failed 0.83% [922] Halobacter failed 0.00% [1406] Celegans3 passed 5.45% [1320] Deinococcu failed 0.42% [1920] 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 9570 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. 42 Mycoplasma 0.00000 0.39365 1.26173 1.32950 1.21585 1.25111 1.35749 1.34895 1.39004 1.36556 1.22049 1.16351 1.18543 1.34464 1.35616 1.40047 1.41101 1.23355 2.53443 2.46558 2.40783 2.51113 2.45655 2.40213 2.39226 2.66113 2.65802 2.10335 2.11713 2.12872 2.14234 2.10236 2.01851 1.92200 1.72742 1.88889 1.62207 1.83902 1.94449 1.81069 1.79181 2.26744 Mycoplasm2 0.39365 0.00000 1.24040 1.35297 1.34757 1.34047 1.40696 1.45172 1.29803 1.34918 1.25876 1.06205 1.25092 1.37979 1.36732 1.44272 1.49140 1.30880 2.44363 2.52643 2.43948 2.56651 2.52279 2.48614 2.46192 2.66615 2.61790 2.18720 2.19141 2.12539 2.21033 2.18534 2.17012 1.96107 1.64079 1.82677 1.74240 1.88858 2.14592 1.81640 1.78523 2.12474 Aquifex 1.26173 1.24040 0.00000 0.65182 0.73517 0.78154 0.89435 0.84773 1.00550 0.81985 1.07001 0.98481 0.76698 0.92822 0.90906 0.93486 1.08136 0.96081 2.13331 2.24552 2.06892 2.05817 2.56766 2.33265 2.51121 2.41564 2.44217 2.05017 2.05476 2.05219 2.14383 2.14128 2.11729 1.96672 1.66454 1.63990 1.47587 1.56363 1.95101 1.83214 1.70056 1.77913 Thermotoga 1.32950 1.35297 0.65182 0.00000 0.86399 0.86057 0.99479 0.94877 1.13038 0.95642 1.08853 1.10750 0.86510 1.00301 0.98181 0.96125 1.17058 1.06766 2.30908 2.41154 2.09903 2.19864 2.48920 2.29146 2.44119 2.47466 2.51891 2.18631 2.19129 2.28102 2.23204 2.24508 2.24138 2.21583 1.67792 1.60569 1.56099 1.58309 1.91555 1.90719 1.67877 1.79914 Bacillus2 1.21585 1.34757 0.73517 0.86399 0.00000 0.66832 0.76874 0.78171 1.01562 0.84252 0.96418 0.99062 0.81426 1.01130 0.89031 0.91201 1.10041 1.06511 2.23527 2.22585 2.09475 2.17879 2.52910 2.36577 2.50758 2.40500 2.63721 2.15509 2.18864 2.10768 2.24051 2.26500 2.18291 2.06879 1.58843 1.59368 1.51664 1.75002 1.92160 1.76229 1.60334 1.75718 Synechocys 1.25111 1.34047 0.78154 0.86057 0.66832 0.00000 0.91202 0.84634 0.98203 0.89914 1.03668 1.04390 0.80034 0.94852 0.96211 0.99114 1.07958 1.06058 2.19223 2.32968 2.08247 2.11284 2.40492 2.18940 2.34790 2.28685 2.46242 2.19070 2.20517 2.23323 2.24290 2.19553 2.09762 2.08751 1.57857 1.56128 1.45484 1.69613 1.80790 1.88249 1.66245 1.77739 Haemophilu 1.35749 1.40696 0.89435 0.99479 0.76874 0.91202 0.00000 0.30511 0.76763 0.95677 1.10267 1.10291 0.92356 0.97656 1.00018 1.03732 1.10937 1.06026 2.35082 2.30776 2.18108 2.09238 2.47383 2.36185 2.32060 2.36013 2.61978 2.09995 2.08469 2.13317 2.09535 2.21946 2.32976 2.18227 1.54146 1.56139 1.52426 1.76380 1.88386 1.76653 1.63215 1.71351 Ecoli 1.34895 1.45172 0.84773 0.94877 0.78171 0.84634 0.30511 0.00000 0.76554 0.88896 1.10161 1.12246 0.92836 0.99963 1.00857 0.97530 1.13758 1.06949 2.28785 2.30902 2.16241 2.09695 2.40887 2.18995 2.36239 2.40514 2.57568 2.08054 2.06201 2.15079 2.00244 2.10018 2.20197 2.09708 1.55086 1.52229 1.47248 1.73415 1.89551 1.77965 1.74896 1.77744 Buchnera 1.39004 1.29803 1.00550 1.13038 1.01562 0.98203 0.76763 0.76554 0.00000 1.05066 1.21507 1.05648 1.18075 1.23878 1.11062 1.14379 1.22759 1.07115 2.24165 2.38398 2.14387 2.22709 2.45308 2.37392 2.41262 2.33748 2.39802 2.02359 2.03864 2.20773 2.14205 2.19644 2.22009 2.07904 1.65310 1.62957 1.64376 1.90698 2.11437 1.98000 1.60393 1.96954 Helicobact 1.36556 1.34918 0.81985 0.95642 0.84252 0.89914 0.95677 0.88896 1.05066 0.00000 1.16628 1.00094 0.92120 1.04589 0.98195 1.03435 1.09677 1.12066 2.16997 2.36776 2.09078 2.10492 2.31069 2.20427 2.37204 2.30448 2.46731 2.23416 2.22516 2.14139 2.11680 2.30014 2.23353 2.07130 1.60713 1.70578 1.64326 1.62637 1.93379 1.83262 1.61433 1.78867 Treponema 1.22049 1.25876 1.07001 1.08853 0.96418 1.03668 1.10267 1.10161 1.21507 1.16628 0.00000 0.89821 0.87797 1.06400 1.05381 1.01406 1.19275 1.21482 2.27390 2.20566 2.08978 2.18694 2.47226 2.44740 2.43995 2.56637 2.46371 1.95057 1.94009 2.05137 2.09494 2.15082 1.94586 1.98017 1.76154 1.75901 1.65466 1.87607 1.93548 1.93355 1.61675 1.78804 Borrelia 1.16351 1.06205 0.98481 1.10750 0.99062 1.04390 1.10291 1.12246 1.05648 1.00094 0.89821 0.00000 0.97571 1.14102 1.05634 1.14681 1.09905 1.01287 2.38436 2.45142 2.28124 2.43334 2.58434 2.37789 2.47945 2.44225 2.50830 1.96332 1.94845 1.97479 2.09927 2.03238 1.99395 2.01088 1.71262 1.80182 1.77190 1.82694 2.17208 2.04360 1.40405 1.94003 Thermus2 1.18543 1.25092 0.76698 0.86510 0.81426 0.80034 0.92356 0.92836 1.18075 0.92120 0.87797 0.97571 0.00000 0.87049 0.91496 0.89538 1.15260 1.13771 2.09943 2.29488 1.96443 2.18695 2.51260 2.30949 2.40023 2.39208 2.41956 2.11651 2.14945 2.24637 2.34535 2.23647 2.08943 2.00982 1.56982 1.59464 1.50871 1.69201 2.03126 1.83245 1.59166 1.87128 Mycobacter 1.34464 1.37979 0.92822 1.00301 1.01130 0.94852 0.97656 0.99963 1.23878 1.04589 1.06400 1.14102 0.87049 0.00000 1.11892 1.08980 1.11790 1.14030 2.32420 2.24159 2.18895 2.26413 2.54706 2.33522 2.47450 2.30711 2.50893 2.27857 2.26928 2.32164 2.33531 2.35999 2.34905 2.21695 1.76015 1.74439 1.70920 1.91698 1.93759 1.88379 1.64440 1.64011 Chlamydoph 1.35616 1.36732 0.90906 0.98181 0.89031 0.96211 1.00018 1.00857 1.11062 0.98195 1.05381 1.05634 0.91496 1.11892 0.00000 0.25427 1.09780 1.17014 2.42595 2.38123 2.16337 2.21465 2.51306 2.38183 2.59441 2.32376 2.49079 2.09648 2.07069 2.00742 2.06256 2.13418 1.94287 2.08298 1.54969 1.61026 1.61700 1.79089 1.85829 1.93537 1.70444 1.65683 Chlamydia 1.40047 1.44272 0.93486 0.96125 0.91201 0.99114 1.03732 0.97530 1.14379 1.03435 1.01406 1.14681 0.89538 1.08980 0.25427 0.00000 1.16386 1.13868 2.38526 2.32435 2.16235 2.26237 2.54109 2.39292 2.57326 2.29286 2.48959 2.01830 2.00589 2.01692 2.05209 2.16403 1.99612 2.03139 1.63839 1.60563 1.65074 1.84466 1.96302 2.00036 1.76037 1.67172 Rickettsia 1.41101 1.49140 1.08136 1.17058 1.10041 1.07958 1.10937 1.13758 1.22759 1.09677 1.19275 1.09905 1.15260 1.11790 1.09780 1.16386 0.00000 1.23088 2.51449 2.50960 2.29592 2.46135 2.54648 2.37535 2.47378 2.49265 2.81334 2.08533 2.08219 2.02205 2.05240 2.23560 2.23966 2.07348 1.58693 1.76578 1.68002 1.84886 2.01424 2.02302 1.75695 1.64925 Mycoplasm3 1.23355 1.30880 0.96081 1.06766 1.06511 1.06058 1.06026 1.06949 1.07115 1.12066 1.21482 1.01287 1.13771 1.14030 1.17014 1.13868 1.23088 0.00000 2.46483 2.50256 2.42662 2.31560 2.72509 2.50041 2.79633 2.46633 2.64543 2.07041 2.06145 2.00832 2.06082 2.09569 2.07304 2.13688 1.81194 1.78927 1.89596 2.01202 2.24918 2.04967 1.58147 1.83928 Lactobacil 2.53443 2.44363 2.13331 2.30908 2.23527 2.19223 2.35082 2.28785 2.24165 2.16997 2.27390 2.38436 2.09943 2.32420 2.42595 2.38526 2.51449 2.46483 0.00000 0.73417 0.68323 1.08365 1.69088 1.54644 1.67058 1.53588 1.57045 1.81044 1.81901 1.87170 1.84609 1.86353 1.83172 1.88246 1.58391 1.59873 1.57349 1.47859 1.72459 1.60272 2.53976 1.75625 Thermus 2.46558 2.52643 2.24552 2.41154 2.22585 2.32968 2.30776 2.30902 2.38398 2.36776 2.20566 2.45142 2.29488 2.24159 2.38123 2.32435 2.50960 2.50256 0.73417 0.00000 0.69355 1.09566 1.62013 1.43530 1.59820 1.51219 1.62373 1.79281 1.81521 1.76532 1.88910 1.82730 1.81021 1.83237 1.61285 1.51888 1.57376 1.60589 1.80072 1.59882 2.83308 1.59717 Bacillus 2.40783 2.43948 2.06892 2.09903 2.09475 2.08247 2.18108 2.16241 2.14387 2.09078 2.08978 2.28124 1.96443 2.18895 2.16337 2.16235 2.29592 2.42662 0.68323 0.69355 0.00000 1.00351 1.57182 1.40653 1.51400 1.34620 1.47170 1.73315 1.74312 1.78653 1.80507 1.78446 1.75421 1.85250 1.44785 1.48947 1.47812 1.42462 1.56792 1.51278 2.48979 1.62959 Pyrococcus 2.51113 2.56651 2.05817 2.19864 2.17879 2.11284 2.09238 2.09695 2.22709 2.10492 2.18694 2.43334 2.18695 2.26413 2.21465 2.26237 2.46135 2.31560 1.08365 1.09566 1.00351 0.00000 1.56125 1.41203 1.45043 1.44112 1.48640 1.70585 1.73242 1.78325 1.73054 1.75359 1.67458 1.64665 1.37050 1.43973 1.37675 1.31483 1.64768 1.48084 2.86342 1.46261 Brugia 2.45655 2.52279 2.56766 2.48920 2.52910 2.40492 2.47383 2.40887 2.45308 2.31069 2.47226 2.58434 2.51260 2.54706 2.51306 2.54109 2.54648 2.72509 1.69088 1.62013 1.57182 1.56125 0.00000 0.48552 0.76943 1.02931 0.96896 2.06903 2.08783 2.20722 1.98479 2.24252 2.27121 2.25709 1.87062 1.85678 1.94058 1.75333 1.89004 1.92814 3.09768 1.99740 Celegans 2.40213 2.48614 2.33265 2.29146 2.36577 2.18940 2.36185 2.18995 2.37392 2.20427 2.44740 2.37789 2.30949 2.33522 2.38183 2.39292 2.37535 2.50041 1.54644 1.43530 1.40653 1.41203 0.48552 0.00000 0.67069 0.83371 0.82877 2.03142 2.03537 1.98743 1.93369 2.05837 2.12608 2.05851 1.82396 1.84748 1.86842 1.69022 1.77586 1.83352 2.74847 1.78814 Homosapien 2.39226 2.46192 2.51121 2.44119 2.50758 2.34790 2.32060 2.36239 2.41262 2.37204 2.43995 2.47945 2.40023 2.47450 2.59441 2.57326 2.47378 2.79633 1.67058 1.59820 1.51400 1.45043 0.76943 0.67069 0.00000 0.80347 0.85991 1.98790 1.96299 2.00958 1.93104 2.15446 2.19226 2.12099 1.87395 1.78678 1.86538 1.74796 1.79271 1.99526 3.05479 1.94634 Saccharomy 2.66113 2.66615 2.41564 2.47466 2.40500 2.28685 2.36013 2.40514 2.33748 2.30448 2.56637 2.44225 2.39208 2.30711 2.32376 2.29286 2.49265 2.46633 1.53588 1.51219 1.34620 1.44112 1.02931 0.83371 0.80347 0.00000 0.65051 1.93299 1.94904 1.93260 1.91663 2.17532 2.00428 2.14026 1.75156 1.64992 1.80631 1.84230 1.67789 1.89912 2.64466 2.00452 Schizosacc 2.65802 2.61790 2.44217 2.51891 2.63721 2.46242 2.61978 2.57568 2.39802 2.46731 2.46371 2.50830 2.41956 2.50893 2.49079 2.48959 2.81334 2.64543 1.57045 1.62373 1.47170 1.48640 0.96896 0.82877 0.85991 0.65051 0.00000 2.03237 2.05663 2.06371 2.03704 2.05955 2.20518 2.20248 1.80120 1.70623 1.86702 1.91273 1.78826 1.92231 3.12841 1.97581 Homosapie2 2.10335 2.18720 2.05017 2.18631 2.15509 2.19070 2.09995 2.08054 2.02359 2.23416 1.95057 1.96332 2.11651 2.27857 2.09648 2.01830 2.08533 2.07041 1.81044 1.79281 1.73315 1.70585 2.06903 2.03142 1.98790 1.93299 2.03237 0.00000 0.05030 0.43786 0.51390 0.67615 0.78426 0.89578 1.33310 1.34577 1.26282 1.38965 1.49349 1.59352 2.42572 1.60257 Rattusnorv 2.11713 2.19141 2.05476 2.19129 2.18864 2.20517 2.08469 2.06201 2.03864 2.22516 1.94009 1.94845 2.14945 2.26928 2.07069 2.00589 2.08219 2.06145 1.81901 1.81521 1.74312 1.73242 2.08783 2.03537 1.96299 1.94904 2.05663 0.05030 0.00000 0.43283 0.51706 0.67594 0.77969 0.90566 1.34477 1.34472 1.28293 1.38582 1.50491 1.61619 2.47541 1.69185 Drosophila 2.12872 2.12539 2.05219 2.28102 2.10768 2.23323 2.13317 2.15079 2.20773 2.14139 2.05137 1.97479 2.24637 2.32164 2.00742 2.01692 2.02205 2.00832 1.87170 1.76532 1.78653 1.78325 2.20722 1.98743 2.00958 1.93260 2.06371 0.43786 0.43283 0.00000 0.54024 0.74270 0.81338 0.95200 1.33037 1.39596 1.27583 1.44376 1.43689 1.66905 2.44969 1.62179 Celegans2 2.14234 2.21033 2.14383 2.23204 2.24051 2.24290 2.09535 2.00244 2.14205 2.11680 2.09494 2.09927 2.34535 2.33531 2.06256 2.05209 2.05240 2.06082 1.84609 1.88910 1.80507 1.73054 1.98479 1.93369 1.93104 1.91663 2.03704 0.51390 0.51706 0.54024 0.00000 0.77899 0.83897 1.02606 1.32219 1.38045 1.35957 1.44196 1.47127 1.60599 2.49692 1.90220 Saccharom2 2.10236 2.18534 2.14128 2.24508 2.26500 2.19553 2.21946 2.10018 2.19644 2.30014 2.15082 2.03238 2.23647 2.35999 2.13418 2.16403 2.23560 2.09569 1.86353 1.82730 1.78446 1.75359 2.24252 2.05837 2.15446 2.17532 2.05955 0.67615 0.67594 0.74270 0.77899 0.00000 0.59836 0.97659 1.34901 1.39279 1.32352 1.41914 1.61236 1.62939 2.31367 1.88086 Schizosac2 2.01851 2.17012 2.11729 2.24138 2.18291 2.09762 2.32976 2.20197 2.22009 2.23353 1.94586 1.99395 2.08943 2.34905 1.94287 1.99612 2.23966 2.07304 1.83172 1.81021 1.75421 1.67458 2.27121 2.12608 2.19226 2.00428 2.20518 0.78426 0.77969 0.81338 0.83897 0.59836 0.00000 0.94147 1.31865 1.38514 1.29214 1.33653 1.50766 1.55352 2.34310 1.81757 Arabidopsi 1.92200 1.96107 1.96672 2.21583 2.06879 2.08751 2.18227 2.09708 2.07904 2.07130 1.98017 2.01088 2.00982 2.21695 2.08298 2.03139 2.07348 2.13688 1.88246 1.83237 1.85250 1.64665 2.25709 2.05851 2.12099 2.14026 2.20248 0.89578 0.90566 0.95200 1.02606 0.97659 0.94147 0.00000 1.34028 1.35664 1.33436 1.31765 1.45733 1.53498 2.38959 1.90772 Methanococ 1.72742 1.64079 1.66454 1.67792 1.58843 1.57857 1.54146 1.55086 1.65310 1.60713 1.76154 1.71262 1.56982 1.76015 1.54969 1.63839 1.58693 1.81194 1.58391 1.61285 1.44785 1.37050 1.87062 1.82396 1.87395 1.75156 1.80120 1.33310 1.34477 1.33037 1.32219 1.34901 1.31865 1.34028 0.00000 0.51004 0.55242 0.64004 0.83668 1.18134 2.15736 1.29462 Methanobac 1.88889 1.82677 1.63990 1.60569 1.59368 1.56128 1.56139 1.52229 1.62957 1.70578 1.75901 1.80182 1.59464 1.74439 1.61026 1.60563 1.76578 1.78927 1.59873 1.51888 1.48947 1.43973 1.85678 1.84748 1.78678 1.64992 1.70623 1.34577 1.34472 1.39596 1.38045 1.39279 1.38514 1.35664 0.51004 0.00000 0.59497 0.68086 0.84338 1.16265 2.24878 1.33755 Archaeoglo 1.62207 1.74240 1.47587 1.56099 1.51664 1.45484 1.52426 1.47248 1.64376 1.64326 1.65466 1.77190 1.50871 1.70920 1.61700 1.65074 1.68002 1.89596 1.57349 1.57376 1.47812 1.37675 1.94058 1.86842 1.86538 1.80631 1.86702 1.26282 1.28293 1.27583 1.35957 1.32352 1.29214 1.33436 0.55242 0.59497 0.00000 0.61798 0.76688 1.09337 2.20361 1.21286 Pyrococcu2 1.83902 1.88858 1.56363 1.58309 1.75002 1.69613 1.76380 1.73415 1.90698 1.62637 1.87607 1.82694 1.69201 1.91698 1.79089 1.84466 1.84886 2.01202 1.47859 1.60589 1.42462 1.31483 1.75333 1.69022 1.74796 1.84230 1.91273 1.38965 1.38582 1.44376 1.44196 1.41914 1.33653 1.31765 0.64004 0.68086 0.61798 0.00000 0.87514 1.09110 2.27505 1.27019 Haloferax 1.94449 2.14592 1.95101 1.91555 1.92160 1.80790 1.88386 1.89551 2.11437 1.93379 1.93548 2.17208 2.03126 1.93759 1.85829 1.96302 2.01424 2.24918 1.72459 1.80072 1.56792 1.64768 1.89004 1.77586 1.79271 1.67789 1.78826 1.49349 1.50491 1.43689 1.47127 1.61236 1.50766 1.45733 0.83668 0.84338 0.76688 0.87514 0.00000 1.05349 2.52230 1.18135 Halobacter 1.81069 1.81640 1.83214 1.90719 1.76229 1.88249 1.76653 1.77965 1.98000 1.83262 1.93355 2.04360 1.83245 1.88379 1.93537 2.00036 2.02302 2.04967 1.60272 1.59882 1.51278 1.48084 1.92814 1.83352 1.99526 1.89912 1.92231 1.59352 1.61619 1.66905 1.60599 1.62939 1.55352 1.53498 1.18134 1.16265 1.09337 1.09110 1.05349 0.00000 2.42299 1.22091 Celegans3 1.79181 1.78523 1.70056 1.67877 1.60334 1.66245 1.63215 1.74896 1.60393 1.61433 1.61675 1.40405 1.59166 1.64440 1.70444 1.76037 1.75695 1.58147 2.53976 2.83308 2.48979 2.86342 3.09768 2.74847 3.05479 2.64466 3.12841 2.42572 2.47541 2.44969 2.49692 2.31367 2.34310 2.38959 2.15736 2.24878 2.20361 2.27505 2.52230 2.42299 0.00000 2.54867 Deinococcu 2.26744 2.12474 1.77913 1.79914 1.75718 1.77739 1.71351 1.77744 1.96954 1.78867 1.78804 1.94003 1.87128 1.64011 1.65683 1.67172 1.64925 1.83928 1.75625 1.59717 1.62959 1.46261 1.99740 1.78814 1.94634 2.00452 1.97581 1.60257 1.69185 1.62179 1.90220 1.88086 1.81757 1.90772 1.29462 1.33755 1.21286 1.27019 1.18135 1.22091 2.54867 0.00000 Average distance (over all possible pairs of sequences): 1.75077 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: 111930 Unresolved quartets: 9570 (= 8.5%) 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! :---Saccharom2 :---------99: : :---Schizosac2 : :-97: :---Homosapie2 : : :100: : : :-98: :---Rattusnorv : : : : :-96: :-99: :-------Drosophila : : : : : :-----------Celegans2 : : : :-------------------Arabidopsi : : :---Saccharomy : :-----99: : : :---Schizosacc : :-96: : : : :---Brugia : : : :-99: : : :-98: :---Celegans : : : :-----85: :-------Homosapien :-96: : : : : :---Lactobacil : : : :-90: : : : :-87: :---Thermus : : : : : : : :-94: :-------Bacillus : : : : : :-----------Pyrococcus : : : : :---Haloferax : : :-----54: : : : :---Halobacter : : : : : : :---Methanococ : : : :-59: : :---------57: : :---Methanobac : :-51: : : :-------Archaeoglo : : : : : :-------Pyrococcu2 : : : :-----------Deinococcu : : :---Chlamydoph :---------------------94: : :---Chlamydia : :-92: :---Haemophilu : : :-91: : :-----------------78: :---Ecoli : : : : : :-------Buchnera : : : : :---Bacillus2 : :---------------------73: : : :---Synechocys : : : : :---Aquifex : :---------------------64: : : :---Thermotoga : : : : :---Thermus2 : :---------------------64: : : :---Mycobacter : : : :---------------------------Helicobact : : : :---------------------------Treponema : : : :---------------------------Borrelia : : : :---------------------------Rickettsia : : : :---------------------------Mycoplasm3 : : : :---------------------------Celegans3 : :-------------------------------Mycoplasm2 : :-------------------------------Mycoplasma Quartet puzzling tree (in CLUSTAL W notation): (Mycoplasma,(((((Saccharom2,Schizosac2)99,(((Homosapie2,Rattusnorv)100, Drosophila)98,Celegans2)99)97,Arabidopsi)96,(((Saccharomy, Schizosacc)99,((Brugia,Celegans)99,Homosapien)98)96,((( Lactobacil,Thermus)90,Bacillus)87,Pyrococcus)94)85,((Haloferax, Halobacter)54,((Methanococ,Methanobac)59,Archaeoglo,Pyrococcu2)51, Deinococcu)57)96,(Chlamydoph,Chlamydia)94,((Haemophilu,Ecoli)91, Buchnera)78,(Bacillus2,Synechocys)73,(Aquifex,Thermotoga)64, (Thermus2,Mycobacter)64,Helicobact,Treponema,Borrelia,Rickettsia, Mycoplasm3,Celegans3)92,Mycoplasm2); 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) ********** ********** *******..* ********** ** : 9989 ********** ********** *****..*** ********** ** : 9949 ********** ********** **..****** ********** ** : 9902 ********** ********** ********** *..******* ** : 9889 ********** ********** *******... .********* ** : 9872 ********** ********** *******... ********** ** : 9827 ********** ********** **...***** ********** ** : 9764 ********** ********** *******... ...******* ** : 9722 ********** ********.. .......... .......... *. : 9640 ********** ********** **.....*** ********** ** : 9602 ********** ********** *******... ....****** ** : 9590 ********** ********.. ..******** ********** ** : 9415 ********** ****..**** ********** ********** ** : 9402 **........ .......... .......... .......... .. : 9171 ******..** ********** ********** ********** ** : 9094 ********** ********.. ********** ********** ** : 8953 ********** ********.. .********* ********** ** : 8693 ********** ********.. .......*** ********** ** : 8493 ******...* ********** ********** ********** ** : 7808 ****..**** ********** ********** ********** ** : 7291 **..****** ********** ********** ********** ** : 6419 ********** **..****** ********** ********** ** : 6389 ********** ********** ********** ****..**** ** : 5894 ********** ********** ********** ****...... *. : 5676 ********** ********** ********** ********.. ** : 5373 ********** ********** ********** ****....** ** : 5090 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ********** ********** ********** ********.. *. : 4867 ********** ..******** ********** ********** ** : 4576 ********** ********.. .......... ....****** ** : 4396 ********** ********** ********** ****...*** ** : 4207 ********** ********** ********** *********. *. : 3963 **..*****. ********** ********** ********** ** : 3091 ********** **..**.*** ********** ********** ** : 3087 ********** ********** ********** ****...... ** : 2773 ********** ********** ********** ****..*.** ** : 2580 ********** ***.**.*** ********** ********** ** : 2446 **.******. ********** ********** ********** ** : 2437 **........ **.....*.. .......... .......... *. : 2378 ********** *.******** ********** ********** .* : 2306 ********** *.*****.** ********** ********** ** : 2223 ********** ********.. .......*** ****...... *. : 2088 **........ **.....*** ********** ********** ** : 2072 ********** ********** ********** ****.*.*** ** : 2070 **........ ........** ********** ********** .* : 2066 ********** ..*****.** ********** ********** ** : 2046 ********** ..*****.** ********** ********** .* : 2002 (3309 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. :---32 Saccharom2 :--43 : :---33 Schizosac2 :--47 : : :-28 Homosapie2 : : :--44 : : : :-29 Rattusnorv : : :-45 : : : :---30 Drosophila : :--46 : :---31 Celegans2 :-----48 : :-----34 Arabidopsi :----------61 : : :---26 Saccharomy : : :--49 : : : :---27 Schizosacc : : :------52 : : : : :---23 Brugia : : : : :--50 : : : : : :--24 Celegans : : : :-51 : : : :---25 Homosapien : :----56 : : : :----19 Lactobacil : : : :-53 : : : : :----20 Thermus : : : :---54 : : : : :---21 Bacillus : : :-55 : : :----22 Pyrococcus : : : : :----39 Haloferax : : :--57 : : : :------40 Halobacter : :--60 : : :--35 Methanococ : : :-58 : : : :---36 Methanobac : :--59 : : :---37 Archaeoglo : : : : : :----38 Pyrococcu2 : : : :----------42 Deinococcu : : :--15 Chlamydoph :-----62 : :--16 Chlamydia : : :--7 Haemophilu : :--63 : : :--8 Ecoli :---64 : :-----9 Buchnera : : :---5 Bacillus2 :--65 : :----6 Synechocys : : :---3 Aquifex :--66 : :----4 Thermotoga : : :----13 Thermus2 :--67 : :-----14 Mycobacter :-------68 : :------10 Helicobact : : : :------11 Treponema : : : :------12 Borrelia : : : :-------17 Rickettsia : : : :-------18 Mycoplasm3 : : : :------------41 Celegans3 : :--2 Mycoplasm2 : :--1 Mycoplasma branch length S.E. branch length S.E. Mycoplasma 1 0.18313 0.02609 43 0.14124 0.02792 Mycoplasm2 2 0.21244 0.02728 44 0.20057 0.02562 Aquifex 3 0.27016 0.03040 45 0.05239 0.01887 Thermotoga 4 0.41799 0.03679 46 0.18176 0.03066 Bacillus2 5 0.32464 0.03199 47 0.18619 0.03939 Synechocys 6 0.36695 0.03403 48 0.54028 0.05985 Haemophilu 7 0.15714 0.02118 49 0.12872 0.02860 Ecoli 8 0.15564 0.02126 50 0.17946 0.02841 Buchnera 9 0.49945 0.04059 51 0.10984 0.02804 Helicobact 10 0.61137 0.04457 52 0.68921 0.06801 Treponema 11 0.68332 0.04767 53 0.10794 0.02887 Borrelia 12 0.68691 0.05124 54 0.29307 0.04524 Thermus2 13 0.35510 0.03543 55 0.11036 0.03796 Mycobacter 14 0.56354 0.04460 56 0.36328 0.05256 Chlamydoph 15 0.11777 0.01929 57 0.12465 0.03144 Chlamydia 16 0.13884 0.02014 58 0.11020 0.02448 Rickettsia 17 0.78592 0.05276 59 0.13519 0.03113 Mycoplasm3 18 0.72207 0.05439 60 0.18936 0.04031 Lactobacil 19 0.37539 0.04141 61 1.08576 0.08743 Thermus 20 0.38408 0.04216 62 0.54294 0.04245 Bacillus 21 0.25579 0.03533 63 0.16236 0.02673 Pyrococcus 22 0.45558 0.05015 64 0.32284 0.03399 Brugia 23 0.32106 0.03158 65 0.19442 0.02724 Celegans 24 0.17288 0.02444 66 0.22597 0.02964 Homosapien 25 0.34255 0.03470 67 0.19796 0.03019 Saccharomy 26 0.32628 0.03407 68 0.81330 0.05872 Schizosacc 27 0.32563 0.03409 Homosapie2 28 0.02505 0.00852 Rattusnorv 29 0.02565 0.00859 Drosophila 30 0.23870 0.02756 Celegans2 31 0.31944 0.03238 Saccharom2 32 0.27527 0.03161 Schizosac2 33 0.33553 0.03439 Arabidopsi 34 0.48730 0.04838 Methanococ 35 0.22857 0.02970 Methanobac 36 0.28514 0.03283 Archaeoglo 37 0.28668 0.03351 Pyrococcu2 38 0.36977 0.03778 Haloferax 39 0.39923 0.04459 Halobacter 40 0.65184 0.05731 Celegans3 41 1.34677 0.08555 10 iterations until convergence Deinococcu 42 1.06790 0.11540 log L: -38782.61 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Mycoplasma:0.18313,(((((Saccharom2:0.27527,Schizosac2:0.33553)99:0.14124, (((Homosapie2:0.02505,Rattusnorv:0.02565)100:0.20057,Drosophila:0.23870) 98:0.05239,Celegans2:0.31944)99:0.18176)97:0.18619,Arabidopsi:0.48730) 96:0.54028,(((Saccharomy:0.32628,Schizosacc:0.32563)99:0.12872,( (Brugia:0.32106,Celegans:0.17288)99:0.17946,Homosapien:0.34255)98:0.10984) 96:0.68921,(((Lactobacil:0.37539,Thermus:0.38408)90:0.10794,Bacillus:0.25579) 87:0.29307,Pyrococcus:0.45558)94:0.11036)85:0.36328,((Haloferax:0.39923, Halobacter:0.65184)54:0.12465,((Methanococ:0.22857,Methanobac:0.28514) 59:0.11020,Archaeoglo:0.28668,Pyrococcu2:0.36977)51:0.13519,Deinococcu:1.06790) 57:0.18936)96:1.08576,(Chlamydoph:0.11777,Chlamydia:0.13884)94:0.54294, ((Haemophilu:0.15714,Ecoli:0.15564)91:0.16236,Buchnera:0.49945)78:0.32284, (Bacillus2:0.32464,Synechocys:0.36695)73:0.19442,(Aquifex:0.27016, Thermotoga:0.41799)64:0.22597,(Thermus2:0.35510,Mycobacter:0.56354) 64:0.19796,Helicobact:0.61137,Treponema:0.68332,Borrelia:0.68691, Rickettsia:0.78592,Mycoplasm3:0.72207,Celegans3:1.34677)92:0.81330, Mycoplasm2:0.21244); TIME STAMP Date and time: Fri Jun 18 10:49:37 1999 Runtime: 36941 seconds (= 615.7 minutes = 10.3 hours)