TREE-PUZZLE 5.0 Input file name: test6.phy 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: 60 sequences with 520 amino acid sites Number of constant sites: 71 (= 13.7% of all sites) Number of site patterns: 464 Number of constant site patterns: 17 (= 3.7% of all site patterns) SUBSTITUTION PROCESS Model of substitution: VT (Mueller-Vingron 2000) Amino acid frequencies (estimated from data set): pi(A) = 7.8% pi(R) = 5.1% pi(N) = 2.6% pi(D) = 5.6% pi(C) = 1.0% pi(Q) = 3.4% pi(E) = 7.5% pi(G) = 8.4% pi(H) = 1.1% pi(I) = 6.3% pi(L) = 8.6% pi(K) = 4.7% pi(M) = 3.1% pi(F) = 3.4% pi(P) = 5.5% pi(S) = 6.4% pi(T) = 5.8% pi(W) = 1.2% pi(Y) = 4.0% pi(V) = 8.7% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 0.63 (S.E. 0.02) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0195 0.1250 2 0.1098 0.1250 3 0.2545 0.1250 4 0.4598 0.1250 5 0.7468 0.1250 6 1.1643 0.1250 7 1.8429 0.1250 8 3.4024 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 1.58. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value aPyrococcu passed 21.78% hPyrococcu passed 31.56% fPyrococcu passed 35.41% Thermococc passed 33.42% Desulfuroc passed 40.19% jMethanoco passed 36.24% Methanobac passed 50.83% aThermopla passed 90.53% vThermopla passed 60.89% BMethanosa passed 97.93% MMethanosa passed 90.15% Archaeoglo passed 25.05% sHalobacte failed 1.19% 1NHalobact failed 1.23% Haloferax_ passed 8.24% pyStreptoc passed 25.36% pnStreptoc passed 95.73% Clostridiu passed 65.36% aSulfolobu passed 64.26% Sulfolobus passed 62.55% sSulfolobu passed 42.50% Aeropyrum_ passed 35.43% 2Treponema passed 13.48% Gossypium_ passed 95.05% Prunus_per passed 99.71% Citrus_uns passed 98.68% Brassica_n passed 98.06% Arabidopsi passed 98.86% Daucus_car passed 99.02% Vigna_radi passed 98.62% Beta_vulga passed 96.38% Mesembryan passed 99.12% Hordeum_vu passed 98.92% 1Acetabula passed 99.99% 2Acetabula passed 99.97% Scherffeli passed 95.25% Cyanidium_ passed 98.43% Bos_taurus passed 99.95% Sus_scrofa passed 99.99% 1Homo_sapi passed 99.89% A1Gallus_g passed 99.96% Fundulus_h passed 99.99% Manduca_se passed 99.84% Drosophila passed 99.63% Caenorhabd passed 99.96% Ascidia_sy passed 88.22% Trypanosom passed 99.67% Plasmodium passed 15.87% Entamoeba_ passed 97.75% Dictyostel passed 49.36% Eremotheci passed 89.61% Saccharomy passed 96.98% Candida_tr passed 95.73% Neurospora passed 94.45% Aspergillu passed 90.38% Schizosacc passed 88.66% Nosema_loc passed 50.86% Giardia_in passed 15.96% Deinococcu passed 78.12% 1Treponema failed 0.21% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. 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. 60 aPyrococcu 0.00000 0.01755 0.04679 0.10196 0.11351 0.40334 0.50882 0.72367 0.62454 0.65769 0.65431 0.55334 0.80479 0.79870 0.73756 0.70486 0.73068 0.61668 0.72317 0.71617 0.79435 0.63201 1.02241 1.05342 1.08878 1.06632 1.04752 1.06447 1.03689 1.04368 1.04964 1.01493 1.04236 1.00196 0.94439 1.07148 1.02173 1.05105 1.08138 1.07144 1.07185 1.04151 1.02789 1.16373 1.05535 1.03795 1.08040 1.21070 1.09690 1.08140 1.07754 1.10187 1.12700 1.06641 1.20615 1.25448 1.24197 1.47858 0.86044 1.86086 hPyrococcu 0.01755 0.00000 0.06124 0.10552 0.11710 0.40664 0.51073 0.74201 0.63558 0.66866 0.65828 0.56103 0.82165 0.81549 0.75003 0.70550 0.72865 0.60441 0.72665 0.71961 0.79184 0.62696 1.02501 1.07457 1.11032 1.08554 1.06581 1.08304 1.05801 1.06426 1.06213 1.03578 1.06122 1.00518 0.96333 1.09023 1.02620 1.05985 1.09039 1.08038 1.07663 1.05279 1.04170 1.17792 1.07169 1.04936 1.09546 1.22622 1.11391 1.10143 1.10206 1.12310 1.14262 1.08229 1.21762 1.26064 1.25430 1.49047 0.85500 1.86191 fPyrococcu 0.04679 0.06124 0.00000 0.10334 0.10757 0.39618 0.48680 0.70973 0.61941 0.64210 0.66988 0.53647 0.79427 0.78826 0.74485 0.70193 0.73114 0.63105 0.71581 0.70884 0.79959 0.63180 1.01815 1.04719 1.08695 1.06439 1.05058 1.06758 1.04167 1.05350 1.05269 1.02277 1.03909 0.99684 0.94843 1.07279 1.01879 1.08358 1.11446 1.10444 1.10204 1.07080 1.06051 1.15471 1.09647 1.06586 1.06851 1.21046 1.05946 1.05672 1.12146 1.10482 1.14148 1.06960 1.20229 1.22407 1.24004 1.45737 0.84943 1.81167 Thermococc 0.10196 0.10552 0.10334 0.00000 0.03637 0.43379 0.51939 0.72292 0.63152 0.71302 0.72348 0.58239 0.82796 0.82174 0.79858 0.72253 0.76718 0.66432 0.77225 0.76495 0.81329 0.71638 1.09311 1.09920 1.13082 1.12626 1.10420 1.10404 1.09303 1.10971 1.09531 1.08833 1.09265 1.06426 1.00613 1.15363 1.08859 1.13948 1.17184 1.16132 1.14507 1.14364 1.09788 1.20251 1.16665 1.14370 1.12738 1.29486 1.14658 1.16041 1.13847 1.14758 1.17170 1.11758 1.21020 1.27051 1.28866 1.39290 0.84934 1.89348 Desulfuroc 0.11351 0.11710 0.10757 0.03637 0.00000 0.43306 0.49344 0.74645 0.63984 0.70600 0.72780 0.58361 0.84014 0.83386 0.81267 0.73311 0.75905 0.65263 0.77128 0.76399 0.80833 0.72753 1.08576 1.12226 1.14947 1.15022 1.12674 1.13237 1.11535 1.13240 1.11761 1.10613 1.10946 1.07617 1.01747 1.16352 1.07089 1.14469 1.17708 1.16663 1.15554 1.14668 1.07673 1.19440 1.15311 1.13532 1.14532 1.28196 1.14221 1.16113 1.14184 1.15097 1.17367 1.08621 1.23050 1.25893 1.27836 1.38872 0.83512 1.88687 jMethanoco 0.40334 0.40664 0.39618 0.43379 0.43306 0.00000 0.41780 0.85409 0.69904 0.70261 0.73855 0.58570 0.80990 0.80369 0.77037 0.79191 0.83388 0.66074 0.90316 0.89467 0.86560 0.70231 1.20580 1.08976 1.09844 1.10239 1.08328 1.10277 1.07120 1.08099 1.10658 1.05673 1.07833 1.10827 1.06626 1.13032 1.03253 1.10721 1.12688 1.12959 1.12486 1.13968 1.06189 1.19567 1.10374 1.12031 1.10849 1.30251 1.10901 1.08880 1.08126 1.13840 1.12846 1.14103 1.33377 1.29699 1.20457 1.43562 0.92374 2.14490 Methanobac 0.50882 0.51073 0.48680 0.51939 0.49344 0.41780 0.00000 0.76344 0.70990 0.74298 0.76666 0.66695 0.81461 0.80852 0.77229 0.80320 0.84561 0.68323 0.92841 0.91980 0.86314 0.81043 1.17911 1.01858 1.04155 1.02263 1.03780 1.04746 1.02379 1.02693 1.05021 1.00542 1.05731 1.01533 0.96963 1.09986 1.07106 1.04121 1.05839 1.06593 1.05667 1.04673 1.01505 1.11834 1.04731 1.05310 1.01625 1.23423 1.09972 1.13219 1.14304 1.12468 1.12342 1.16597 1.34491 1.25131 1.27192 1.41461 0.87237 2.22381 aThermopla 0.72367 0.74201 0.70973 0.72292 0.74645 0.85409 0.76344 0.00000 0.18397 0.87807 0.86958 0.79239 1.00236 0.99507 0.92114 0.91484 0.97265 0.85779 1.22289 1.21163 1.15078 1.08960 1.40360 1.28202 1.29850 1.28520 1.28413 1.30384 1.28257 1.29363 1.34084 1.27997 1.27443 1.28595 1.25042 1.31137 1.25918 1.34009 1.33907 1.37123 1.33971 1.35729 1.33472 1.40414 1.35975 1.29831 1.33523 1.52363 1.30188 1.30649 1.36869 1.37788 1.39153 1.41617 1.56929 1.43401 1.43243 1.65069 1.12934 2.43987 vThermopla 0.62454 0.63558 0.61941 0.63152 0.63984 0.69904 0.70990 0.18397 0.00000 0.75806 0.74797 0.66291 0.88072 0.87410 0.85367 0.81648 0.89687 0.74730 1.11133 1.10102 0.99106 0.94735 1.27694 1.18378 1.23401 1.23442 1.21911 1.24003 1.20175 1.20301 1.20738 1.18325 1.19665 1.20354 1.17086 1.16809 1.14943 1.25578 1.26852 1.28582 1.25489 1.27902 1.23209 1.35413 1.25411 1.21245 1.22023 1.33981 1.20151 1.20565 1.24412 1.24852 1.24141 1.27583 1.43300 1.32797 1.28665 1.46823 0.98132 2.31440 BMethanosa 0.65769 0.66866 0.64210 0.71302 0.70600 0.70261 0.74298 0.87807 0.75806 0.00000 0.14374 0.54717 0.62024 0.61498 0.62192 0.91602 0.96177 0.81491 1.14138 1.13094 1.10168 0.93993 1.18858 1.17166 1.21575 1.20546 1.19910 1.20610 1.19386 1.18551 1.22418 1.18191 1.20878 1.29569 1.23044 1.25020 1.12183 1.25159 1.27877 1.28087 1.26119 1.27415 1.21973 1.35713 1.20368 1.24583 1.17637 1.35814 1.08599 1.23351 1.27273 1.29639 1.25800 1.26965 1.41764 1.36369 1.32966 1.65067 0.92072 2.01325 MMethanosa 0.65431 0.65828 0.66988 0.72348 0.72780 0.73855 0.76666 0.86958 0.74797 0.14374 0.00000 0.56842 0.66867 0.66318 0.63081 0.91293 0.95959 0.80850 1.14895 1.13836 1.11686 1.03588 1.25465 1.17278 1.21804 1.17406 1.18039 1.19401 1.16483 1.15673 1.20431 1.14924 1.19754 1.26984 1.19538 1.22582 1.15087 1.24060 1.25388 1.27134 1.24909 1.23101 1.20720 1.35685 1.22230 1.23355 1.21400 1.35151 1.12694 1.26967 1.29651 1.33255 1.29115 1.29401 1.42083 1.37012 1.35036 1.63865 0.95630 2.15012 Archaeoglo 0.55334 0.56103 0.53647 0.58239 0.58361 0.58570 0.66695 0.79239 0.66291 0.54717 0.56842 0.00000 0.75730 0.75142 0.68833 0.85689 0.92822 0.69828 0.94504 0.93617 0.89475 0.81825 1.20814 1.16967 1.21775 1.19731 1.20072 1.20179 1.19442 1.19009 1.23457 1.18276 1.17280 1.18555 1.16250 1.25257 1.18840 1.28709 1.29893 1.32333 1.28584 1.27998 1.19072 1.35706 1.18201 1.24658 1.25333 1.30714 1.12409 1.21798 1.25915 1.26130 1.27461 1.29241 1.47821 1.39906 1.37620 1.58025 0.92838 2.02378 sHalobacte 0.80479 0.82165 0.79427 0.82796 0.84014 0.80990 0.81461 1.00236 0.88072 0.62024 0.66867 0.75730 0.00000 0.00195 0.20960 0.94120 0.97284 0.95482 1.20697 1.19586 1.23319 1.09978 1.34558 1.31351 1.32921 1.29288 1.31685 1.32496 1.29299 1.30151 1.31810 1.29440 1.34335 1.27449 1.22257 1.39726 1.22128 1.23151 1.25766 1.25731 1.25371 1.19896 1.21675 1.39725 1.22956 1.22826 1.31352 1.45281 1.13009 1.36224 1.37184 1.34704 1.36677 1.29681 1.49690 1.38474 1.36257 1.73197 1.10835 2.09844 1NHalobact 0.79870 0.81549 0.78826 0.82174 0.83386 0.80369 0.80852 0.99507 0.87410 0.61498 0.66318 0.75142 0.00195 0.00000 0.20651 0.93437 0.96582 0.94792 1.19850 1.18747 1.22447 1.09196 1.33619 1.30423 1.31983 1.28376 1.30756 1.31561 1.28386 1.29235 1.30884 1.28524 1.33390 1.26558 1.21400 1.38744 1.21267 1.22286 1.24884 1.24848 1.24491 1.19052 1.20816 1.38747 1.22092 1.21957 1.30424 1.44266 1.12200 1.35270 1.36215 1.33757 1.35717 1.28771 1.48640 1.37502 1.35300 1.71964 1.10049 2.09372 Haloferax_ 0.73756 0.75003 0.74485 0.79858 0.81267 0.77037 0.77229 0.92114 0.85367 0.62192 0.63081 0.68833 0.20960 0.20651 0.00000 0.87760 0.92484 0.84264 1.20567 1.19454 1.23125 1.06942 1.28400 1.23591 1.26455 1.23406 1.25220 1.26495 1.23255 1.23245 1.33219 1.22541 1.27795 1.27219 1.23378 1.41346 1.22477 1.17798 1.20332 1.18995 1.20097 1.18464 1.23549 1.37765 1.25451 1.24772 1.25651 1.46671 1.12094 1.29373 1.41106 1.40311 1.41768 1.33123 1.50471 1.42664 1.41273 1.80783 1.04645 2.05741 pyStreptoc 0.70486 0.70550 0.70193 0.72253 0.73311 0.79191 0.80320 0.91484 0.81648 0.91602 0.91293 0.85689 0.94120 0.93437 0.87760 0.00000 0.21581 0.41543 1.07937 1.06263 1.02443 1.10854 1.20830 1.08043 1.13362 1.15929 1.12105 1.13566 1.11022 1.12710 1.11619 1.10715 1.12775 1.18358 1.13565 1.14117 1.06966 1.03289 1.03611 1.07094 1.04230 1.03688 1.06780 1.20309 1.09522 1.09622 1.15501 1.33308 1.17423 1.11256 1.20324 1.25389 1.20209 1.18987 1.48314 1.35640 1.27489 1.60023 1.05987 1.96522 pnStreptoc 0.73068 0.72865 0.73114 0.76718 0.75905 0.83388 0.84561 0.97265 0.89687 0.96177 0.95959 0.92822 0.97284 0.96582 0.92484 0.21581 0.00000 0.44546 1.12657 1.10929 1.09517 1.13949 1.26084 1.12648 1.12477 1.11381 1.13246 1.13335 1.12456 1.11144 1.12475 1.10676 1.11348 1.19556 1.16013 1.16165 1.11212 1.06829 1.08684 1.08873 1.06543 1.06203 1.10184 1.20893 1.14748 1.19514 1.19380 1.31137 1.19721 1.12403 1.26687 1.24951 1.24651 1.31428 1.48529 1.34146 1.25415 1.62200 1.04032 2.11019 Clostridiu 0.61668 0.60441 0.63105 0.66432 0.65263 0.66074 0.68323 0.85779 0.74730 0.81491 0.80850 0.69828 0.95482 0.94792 0.84264 0.41543 0.44546 0.00000 0.96947 0.96049 0.96480 0.96805 1.16091 1.18843 1.20308 1.19847 1.18067 1.19134 1.18822 1.17548 1.20175 1.16624 1.16595 1.14774 1.14372 1.21373 1.11615 1.12946 1.13412 1.15576 1.12942 1.13061 1.10732 1.20276 1.13725 1.13796 1.14664 1.33213 1.22406 1.17552 1.18314 1.19293 1.17782 1.16173 1.33719 1.29357 1.28811 1.55518 0.98819 2.04503 aSulfolobu 0.72317 0.72665 0.71581 0.77225 0.77128 0.90316 0.92841 1.22289 1.11133 1.14138 1.14895 0.94504 1.20697 1.19850 1.20567 1.07937 1.12657 0.96947 0.00000 0.00382 0.24122 0.57633 1.23841 1.34294 1.34244 1.32704 1.31375 1.32927 1.31065 1.32699 1.32460 1.31514 1.41834 1.36872 1.31685 1.42409 1.30131 1.29965 1.30764 1.33524 1.28069 1.27639 1.28061 1.40686 1.25959 1.35542 1.30833 1.52456 1.28384 1.41262 1.29339 1.31198 1.30291 1.23878 1.48457 1.52628 1.51220 1.72429 1.21550 2.24078 Sulfolobus 0.71617 0.71961 0.70884 0.76495 0.76399 0.89467 0.91980 1.21163 1.10102 1.13094 1.13836 0.93617 1.19586 1.18747 1.19454 1.06263 1.10929 0.96049 0.00382 0.00000 0.23466 0.57049 1.22695 1.33038 1.32997 1.31468 1.30150 1.31690 1.29845 1.31465 1.31230 1.30285 1.40516 1.35612 1.30475 1.41088 1.28150 1.27968 1.28755 1.31475 1.26095 1.25675 1.26093 1.38530 1.24020 1.33459 1.28834 1.50115 1.26389 1.39095 1.28133 1.29976 1.29073 1.22732 1.47066 1.51198 1.48914 1.69759 1.20441 2.22019 sSulfolobu 0.79435 0.79184 0.79959 0.81329 0.80833 0.86560 0.86314 1.15078 0.99106 1.10168 1.11686 0.89475 1.23319 1.22447 1.23125 1.02443 1.09517 0.96480 0.24122 0.23466 0.00000 0.59823 1.24429 1.29339 1.33448 1.31042 1.30450 1.31090 1.28476 1.29752 1.29574 1.27263 1.36175 1.29308 1.22772 1.36880 1.28360 1.31558 1.32248 1.36390 1.29485 1.33216 1.27310 1.46149 1.28660 1.38231 1.22184 1.49601 1.28623 1.37297 1.34101 1.31247 1.30796 1.27642 1.53518 1.49610 1.54716 1.73609 1.09731 2.29093 Aeropyrum_ 0.63201 0.62696 0.63180 0.71638 0.72753 0.70231 0.81043 1.08960 0.94735 0.93993 1.03588 0.81825 1.09978 1.09196 1.06942 1.10854 1.13949 0.96805 0.57633 0.57049 0.59823 0.00000 1.13104 1.15497 1.17972 1.18206 1.16326 1.18538 1.17003 1.19364 1.20397 1.13531 1.20875 1.24295 1.20204 1.30115 1.22845 1.25035 1.26521 1.28285 1.25415 1.25577 1.24132 1.36441 1.26090 1.26313 1.18944 1.40198 1.29433 1.33795 1.28220 1.28503 1.30400 1.25388 1.49914 1.39637 1.38657 1.69539 1.08628 2.04599 2Treponema 1.02241 1.02501 1.01815 1.09311 1.08576 1.20580 1.17911 1.40360 1.27694 1.18858 1.25465 1.20814 1.34558 1.33619 1.28400 1.20830 1.26084 1.16091 1.23841 1.22695 1.24429 1.13104 0.00000 1.70742 1.73681 1.73101 1.70237 1.72397 1.72387 1.72096 1.74075 1.71122 1.75945 1.70244 1.66480 1.72103 1.61533 1.65091 1.69852 1.69244 1.66757 1.65674 1.67659 1.73912 1.62579 1.62060 1.61120 1.89083 1.63692 1.78740 1.72521 1.69878 1.75376 1.73516 1.82555 1.85508 1.85179 1.92760 1.33344 2.49952 Gossypium_ 1.05342 1.07457 1.04719 1.09920 1.12226 1.08976 1.01858 1.28202 1.18378 1.17166 1.17278 1.16967 1.31351 1.30423 1.23591 1.08043 1.12648 1.18843 1.34294 1.33038 1.29339 1.15497 1.70742 0.00000 0.04383 0.04117 0.03930 0.05045 0.02796 0.04083 0.05930 0.05131 0.08145 0.29195 0.29217 0.33544 0.37474 0.40112 0.40703 0.41096 0.39317 0.40653 0.40603 0.47758 0.39761 0.44849 0.46388 0.64467 0.55329 0.48096 0.60151 0.58511 0.62150 0.58837 0.69835 0.58862 0.62518 1.05811 1.13545 2.37151 Prunus_per 1.08878 1.11032 1.08695 1.13082 1.14947 1.09844 1.04155 1.29850 1.23401 1.21575 1.21804 1.21775 1.32921 1.31983 1.26455 1.13362 1.12477 1.20308 1.34244 1.32997 1.33448 1.17972 1.73681 0.04383 0.00000 0.04117 0.04153 0.05191 0.03473 0.04710 0.08644 0.07268 0.08715 0.30935 0.30937 0.35611 0.38970 0.41381 0.41248 0.41890 0.40179 0.40151 0.42290 0.48837 0.40735 0.46093 0.49401 0.65596 0.54154 0.48067 0.60511 0.58507 0.62323 0.59765 0.71596 0.60351 0.62799 1.06140 1.13626 2.45873 Citrus_uns 1.06632 1.08554 1.06439 1.12626 1.15022 1.10239 1.02263 1.28520 1.23442 1.20546 1.17406 1.19731 1.29288 1.28376 1.23406 1.15929 1.11381 1.19847 1.32704 1.31468 1.31042 1.18206 1.73101 0.04117 0.04117 0.00000 0.03714 0.05021 0.02404 0.03630 0.06904 0.05586 0.08595 0.31275 0.30804 0.35693 0.37243 0.41754 0.41619 0.42642 0.40783 0.41113 0.41540 0.48338 0.41795 0.46102 0.47514 0.65562 0.54420 0.49204 0.61826 0.59341 0.63400 0.60590 0.72145 0.60061 0.63694 1.06370 1.12079 2.46203 Brassica_n 1.04752 1.06581 1.05058 1.10420 1.12674 1.08328 1.03780 1.28413 1.21911 1.19910 1.18039 1.20072 1.31685 1.30756 1.25220 1.12105 1.13246 1.18067 1.31375 1.30150 1.30450 1.16326 1.70237 0.03930 0.04153 0.03714 0.00000 0.01974 0.02238 0.03691 0.06064 0.05246 0.07160 0.28868 0.28587 0.34544 0.35807 0.40730 0.40595 0.41685 0.39908 0.40233 0.40783 0.48434 0.39898 0.44607 0.47724 0.65574 0.54386 0.47503 0.59747 0.56781 0.61301 0.59312 0.69628 0.58270 0.63224 1.07662 1.11545 2.44654 Arabidopsi 1.06447 1.08304 1.06758 1.10404 1.13237 1.10277 1.04746 1.30384 1.24003 1.20610 1.19401 1.20179 1.32496 1.31561 1.26495 1.13566 1.13335 1.19134 1.32927 1.31690 1.31090 1.18538 1.72397 0.05045 0.05191 0.05021 0.01974 0.00000 0.04148 0.04800 0.07736 0.05934 0.07675 0.27316 0.27639 0.33508 0.37589 0.41552 0.41449 0.42514 0.40390 0.40726 0.39797 0.47646 0.39839 0.44864 0.46844 0.64256 0.55041 0.46486 0.60827 0.58773 0.62267 0.59943 0.71733 0.60428 0.63302 1.06827 1.13034 2.46112 Daucus_car 1.03689 1.05801 1.04167 1.09303 1.11535 1.07120 1.02379 1.28257 1.20175 1.19386 1.16483 1.19442 1.29299 1.28386 1.23255 1.11022 1.12456 1.18822 1.31065 1.29845 1.28476 1.17003 1.72387 0.02796 0.03473 0.02404 0.02238 0.04148 0.00000 0.03009 0.05257 0.04038 0.06785 0.28792 0.28819 0.34211 0.36634 0.40894 0.40760 0.41778 0.40073 0.40142 0.40315 0.48053 0.40605 0.44950 0.47671 0.65749 0.53052 0.48292 0.61099 0.58885 0.62180 0.58369 0.70379 0.58860 0.63261 1.05205 1.11798 2.41282 Vigna_radi 1.04368 1.06426 1.05350 1.10971 1.13240 1.08099 1.02693 1.29363 1.20301 1.18551 1.15673 1.19009 1.30151 1.29235 1.23245 1.12710 1.11144 1.17548 1.32699 1.31465 1.29752 1.19364 1.72096 0.04083 0.04710 0.03630 0.03691 0.04800 0.03009 0.00000 0.06018 0.04958 0.08263 0.28749 0.29388 0.32420 0.36763 0.40549 0.40414 0.41429 0.40088 0.40083 0.39906 0.48278 0.39862 0.46338 0.47827 0.65930 0.54434 0.47958 0.60510 0.58959 0.61772 0.59218 0.71080 0.59490 0.64575 1.07158 1.11264 2.40501 Beta_vulga 1.04964 1.06213 1.05269 1.09531 1.11761 1.10658 1.05021 1.34084 1.20738 1.22418 1.20431 1.23457 1.31810 1.30884 1.33219 1.11619 1.12475 1.20175 1.32460 1.31230 1.29574 1.20397 1.74075 0.05930 0.08644 0.06904 0.06064 0.07736 0.05257 0.06018 0.00000 0.05882 0.10325 0.29544 0.28401 0.36230 0.36922 0.40365 0.40955 0.41448 0.39924 0.41896 0.40452 0.49255 0.40509 0.44357 0.46543 0.65598 0.57578 0.50074 0.61412 0.59840 0.60536 0.61098 0.70863 0.59384 0.66249 1.06465 1.15238 2.46299 Mesembryan 1.01493 1.03578 1.02277 1.08833 1.10613 1.05673 1.00542 1.27997 1.18325 1.18191 1.14924 1.18276 1.29440 1.28524 1.22541 1.10715 1.10676 1.16624 1.31514 1.30285 1.27263 1.13531 1.71122 0.05131 0.07268 0.05586 0.05246 0.05934 0.04038 0.04958 0.05882 0.00000 0.09668 0.29128 0.28849 0.33692 0.37041 0.41346 0.40890 0.42459 0.40290 0.40379 0.40097 0.47658 0.41420 0.45147 0.47592 0.65569 0.55194 0.48119 0.61204 0.59183 0.61412 0.57907 0.70449 0.59976 0.65208 1.07096 1.11385 2.40703 Hordeum_vu 1.04236 1.06122 1.03909 1.09265 1.10946 1.07833 1.05731 1.27443 1.19665 1.20878 1.19754 1.17280 1.34335 1.33390 1.27795 1.12775 1.11348 1.16595 1.41834 1.40516 1.36175 1.20875 1.75945 0.08145 0.08715 0.08595 0.07160 0.07675 0.06785 0.08263 0.10325 0.09668 0.00000 0.28901 0.29730 0.35164 0.36699 0.43339 0.43210 0.44244 0.42379 0.43148 0.43219 0.48343 0.43537 0.47940 0.48196 0.67350 0.56155 0.48789 0.61269 0.59118 0.62632 0.59881 0.70998 0.59527 0.66719 1.10111 1.14665 2.33326 1Acetabula 1.00196 1.00518 0.99684 1.06426 1.07617 1.10827 1.01533 1.28595 1.20354 1.29569 1.26984 1.18555 1.27449 1.26558 1.27219 1.18358 1.19556 1.14774 1.36872 1.35612 1.29308 1.24295 1.70244 0.29195 0.30935 0.31275 0.28868 0.27316 0.28792 0.28749 0.29544 0.29128 0.28901 0.00000 0.02811 0.29530 0.39624 0.42734 0.43016 0.43605 0.43521 0.43035 0.38810 0.45940 0.41628 0.42639 0.47833 0.62340 0.51877 0.48655 0.62159 0.59253 0.60662 0.63145 0.69674 0.58014 0.74311 1.03407 1.21658 2.24359 2Acetabula 0.94439 0.96333 0.94843 1.00613 1.01747 1.06626 0.96963 1.25042 1.17086 1.23044 1.19538 1.16250 1.22257 1.21400 1.23378 1.13565 1.16013 1.14372 1.31685 1.30475 1.22772 1.20204 1.66480 0.29217 0.30937 0.30804 0.28587 0.27639 0.28819 0.29388 0.28401 0.28849 0.29730 0.02811 0.00000 0.27935 0.37902 0.40636 0.40903 0.41722 0.42211 0.41598 0.37082 0.45711 0.40791 0.40344 0.44653 0.59339 0.48618 0.45989 0.60001 0.57012 0.59358 0.60891 0.68042 0.56248 0.70461 0.97696 1.17964 2.16410 Scherffeli 1.07148 1.09023 1.07279 1.15363 1.16352 1.13032 1.09986 1.31137 1.16809 1.25020 1.22582 1.25257 1.39726 1.38744 1.41346 1.14117 1.16165 1.21373 1.42409 1.41088 1.36880 1.30115 1.72103 0.33544 0.35611 0.35693 0.34544 0.33508 0.34211 0.32420 0.36230 0.33692 0.35164 0.29530 0.27935 0.00000 0.43983 0.47398 0.46938 0.49338 0.47501 0.47377 0.45473 0.55334 0.45634 0.48371 0.52416 0.68298 0.56366 0.53921 0.69002 0.68119 0.69932 0.67500 0.82767 0.64497 0.72221 1.05484 1.18834 2.40314 Cyanidium_ 1.02173 1.02620 1.01879 1.08859 1.07089 1.03253 1.07106 1.25918 1.14943 1.12183 1.15087 1.18840 1.22128 1.21267 1.22477 1.06966 1.11212 1.11615 1.30131 1.28150 1.28360 1.22845 1.61533 0.37474 0.38970 0.37243 0.35807 0.37589 0.36634 0.36763 0.36922 0.37041 0.36699 0.39624 0.37902 0.43983 0.00000 0.35799 0.36042 0.37546 0.37427 0.37809 0.40436 0.46431 0.36582 0.42525 0.48885 0.62889 0.50819 0.43513 0.62498 0.61258 0.61310 0.60482 0.75332 0.59636 0.70060 1.01243 1.17998 2.24969 Bos_taurus 1.05105 1.05985 1.08358 1.13948 1.14469 1.10721 1.04121 1.34009 1.25578 1.25159 1.24060 1.28709 1.23151 1.22286 1.17798 1.03289 1.06829 1.12946 1.29965 1.27968 1.31558 1.25035 1.65091 0.40112 0.41381 0.41754 0.40730 0.41552 0.40894 0.40549 0.40365 0.41346 0.43339 0.42734 0.40636 0.47398 0.35799 0.00000 0.01173 0.01362 0.02981 0.06046 0.15601 0.20410 0.18691 0.20597 0.50317 0.66554 0.49849 0.39825 0.47286 0.48728 0.46491 0.52980 0.63435 0.42791 0.59583 1.06247 1.15367 2.35148 Sus_scrofa 1.08138 1.09039 1.11446 1.17184 1.17708 1.12688 1.05839 1.33907 1.26852 1.27877 1.25388 1.29893 1.25766 1.24884 1.20332 1.03611 1.08684 1.13412 1.30764 1.28755 1.32248 1.26521 1.69852 0.40703 0.41248 0.41619 0.40595 0.41449 0.40760 0.40414 0.40955 0.40890 0.43210 0.43016 0.40903 0.46938 0.36042 0.01173 0.00000 0.02575 0.03834 0.06978 0.16729 0.20829 0.19363 0.21867 0.51406 0.67576 0.51239 0.40421 0.48900 0.50267 0.48554 0.54375 0.65914 0.44818 0.60054 1.09103 1.19145 2.32079 1Homo_sapi 1.07144 1.08038 1.10444 1.16132 1.16663 1.12959 1.06593 1.37123 1.28582 1.28087 1.27134 1.32333 1.25731 1.24848 1.18995 1.07094 1.08873 1.15576 1.33524 1.31475 1.36390 1.28285 1.69244 0.41096 0.41890 0.42642 0.41685 0.42514 0.41778 0.41429 0.41448 0.42459 0.44244 0.43605 0.41722 0.49338 0.37546 0.01362 0.02575 0.00000 0.04019 0.06720 0.16660 0.21481 0.20248 0.22194 0.51705 0.69098 0.51467 0.40678 0.49152 0.49278 0.48459 0.54558 0.65472 0.44780 0.61875 1.08642 1.17707 2.39001 A1Gallus_g 1.07185 1.07663 1.10204 1.14507 1.15554 1.12486 1.05667 1.33971 1.25489 1.26119 1.24909 1.28584 1.25371 1.24491 1.20097 1.04230 1.06543 1.12942 1.28069 1.26095 1.29485 1.25415 1.66757 0.39317 0.40179 0.40783 0.39908 0.40390 0.40073 0.40088 0.39924 0.40290 0.42379 0.43521 0.42211 0.47501 0.37427 0.02981 0.03834 0.04019 0.00000 0.06759 0.17207 0.21564 0.20316 0.22438 0.49664 0.66052 0.51428 0.39035 0.48639 0.48987 0.47540 0.54852 0.64199 0.44642 0.60934 1.05992 1.13838 2.35238 Fundulus_h 1.04151 1.05279 1.07080 1.14364 1.14668 1.13968 1.04673 1.35729 1.27902 1.27415 1.23101 1.27998 1.19896 1.19052 1.18464 1.03688 1.06203 1.13061 1.27639 1.25675 1.33216 1.25577 1.65674 0.40653 0.40151 0.41113 0.40233 0.40726 0.40142 0.40083 0.41896 0.40379 0.43148 0.43035 0.41598 0.47377 0.37809 0.06046 0.06978 0.06720 0.06759 0.00000 0.15615 0.21491 0.19367 0.22156 0.53167 0.67150 0.48614 0.39451 0.48689 0.48158 0.47294 0.54890 0.65048 0.44236 0.62261 1.05494 1.14975 2.34730 Manduca_se 1.02789 1.04170 1.06051 1.09788 1.07673 1.06189 1.01505 1.33472 1.23209 1.21973 1.20720 1.19072 1.21675 1.20816 1.23549 1.06780 1.10184 1.10732 1.28061 1.26093 1.27310 1.24132 1.67659 0.40603 0.42290 0.41540 0.40783 0.39797 0.40315 0.39906 0.40452 0.40097 0.43219 0.38810 0.37082 0.45473 0.40436 0.15601 0.16729 0.16660 0.17207 0.15615 0.00000 0.14232 0.20039 0.21891 0.53394 0.64245 0.49469 0.41604 0.46248 0.48437 0.45841 0.52406 0.63012 0.47441 0.58028 1.03624 1.18311 2.35989 Drosophila 1.16373 1.17792 1.15471 1.20251 1.19440 1.19567 1.11834 1.40414 1.35413 1.35713 1.35685 1.35706 1.39725 1.38747 1.37765 1.20309 1.20893 1.20276 1.40686 1.38530 1.46149 1.36441 1.73912 0.47758 0.48837 0.48338 0.48434 0.47646 0.48053 0.48278 0.49255 0.47658 0.48343 0.45940 0.45711 0.55334 0.46431 0.20410 0.20829 0.21481 0.21564 0.21491 0.14232 0.00000 0.26332 0.27836 0.57955 0.72080 0.54262 0.46297 0.59504 0.59621 0.57553 0.61971 0.73564 0.53314 0.65860 1.15509 1.29238 2.61978 Caenorhabd 1.05535 1.07169 1.09647 1.16665 1.15311 1.10374 1.04731 1.35975 1.25411 1.20368 1.22230 1.18201 1.22956 1.22092 1.25451 1.09522 1.14748 1.13725 1.25959 1.24020 1.28660 1.26090 1.62579 0.39761 0.40735 0.41795 0.39898 0.39839 0.40605 0.39862 0.40509 0.41420 0.43537 0.41628 0.40791 0.45634 0.36582 0.18691 0.19363 0.20248 0.20316 0.19367 0.20039 0.26332 0.00000 0.26362 0.52027 0.65787 0.51586 0.39561 0.49222 0.50823 0.50491 0.50976 0.60260 0.46497 0.62040 1.03226 1.16306 2.44669 Ascidia_sy 1.03795 1.04936 1.06586 1.14370 1.13532 1.12031 1.05310 1.29831 1.21245 1.24583 1.23355 1.24658 1.22826 1.21957 1.24772 1.09622 1.19514 1.13796 1.35542 1.33459 1.38231 1.26313 1.62060 0.44849 0.46093 0.46102 0.44607 0.44864 0.44950 0.46338 0.44357 0.45147 0.47940 0.42639 0.40344 0.48371 0.42525 0.20597 0.21867 0.22194 0.22438 0.22156 0.21891 0.27836 0.26362 0.00000 0.52728 0.67845 0.58551 0.41808 0.50220 0.49621 0.49037 0.52591 0.66579 0.46082 0.65946 1.10590 1.14752 2.36999 Trypanosom 1.08040 1.09546 1.06851 1.12738 1.14532 1.10849 1.01625 1.33523 1.22023 1.17637 1.21400 1.25333 1.31352 1.30424 1.25651 1.15501 1.19380 1.14664 1.30833 1.28834 1.22184 1.18944 1.61120 0.46388 0.49401 0.47514 0.47724 0.46844 0.47671 0.47827 0.46543 0.47592 0.48196 0.47833 0.44653 0.52416 0.48885 0.50317 0.51406 0.51705 0.49664 0.53167 0.53394 0.57955 0.52027 0.52728 0.00000 0.62924 0.54748 0.49514 0.66083 0.65025 0.63179 0.71333 0.76567 0.63096 0.79573 1.05678 1.16657 2.45598 Plasmodium 1.21070 1.22622 1.21046 1.29486 1.28196 1.30251 1.23423 1.52363 1.33981 1.35814 1.35151 1.30714 1.45281 1.44266 1.46671 1.33308 1.31137 1.33213 1.52456 1.50115 1.49601 1.40198 1.89083 0.64467 0.65596 0.65562 0.65574 0.64256 0.65749 0.65930 0.65598 0.65569 0.67350 0.62340 0.59339 0.68298 0.62889 0.66554 0.67576 0.69098 0.66052 0.67150 0.64245 0.72080 0.65787 0.67845 0.62924 0.00000 0.68593 0.65913 0.83107 0.83043 0.81325 0.83323 0.98020 0.79721 0.92734 1.10371 1.22799 2.78115 Entamoeba_ 1.09690 1.11391 1.05946 1.14658 1.14221 1.10901 1.09972 1.30188 1.20151 1.08599 1.12694 1.12409 1.13009 1.12200 1.12094 1.17423 1.19721 1.22406 1.28384 1.26389 1.28623 1.29433 1.63692 0.55329 0.54154 0.54420 0.54386 0.55041 0.53052 0.54434 0.57578 0.55194 0.56155 0.51877 0.48618 0.56366 0.50819 0.49849 0.51239 0.51467 0.51428 0.48614 0.49469 0.54262 0.51586 0.58551 0.54748 0.68593 0.00000 0.51316 0.68766 0.67613 0.68534 0.71295 0.78338 0.64503 0.75500 1.07862 1.11721 2.20155 Dictyostel 1.08140 1.10143 1.05672 1.16041 1.16113 1.08880 1.13219 1.30649 1.20565 1.23351 1.26967 1.21798 1.36224 1.35270 1.29373 1.11256 1.12403 1.17552 1.41262 1.39095 1.37297 1.33795 1.78740 0.48096 0.48067 0.49204 0.47503 0.46486 0.48292 0.47958 0.50074 0.48119 0.48789 0.48655 0.45989 0.53921 0.43513 0.39825 0.40421 0.40678 0.39035 0.39451 0.41604 0.46297 0.39561 0.41808 0.49514 0.65913 0.51316 0.00000 0.55153 0.52871 0.57553 0.60488 0.72707 0.54575 0.69542 1.13822 1.14102 2.51694 Eremotheci 1.07754 1.10206 1.12146 1.13847 1.14184 1.08126 1.14304 1.36869 1.24412 1.27273 1.29651 1.25915 1.37184 1.36215 1.41106 1.20324 1.26687 1.18314 1.29339 1.28133 1.34101 1.28220 1.72521 0.60151 0.60511 0.61826 0.59747 0.60827 0.61099 0.60510 0.61412 0.61204 0.61269 0.62159 0.60001 0.69002 0.62498 0.47286 0.48900 0.49152 0.48639 0.48689 0.46248 0.59504 0.49222 0.50220 0.66083 0.83107 0.68766 0.55153 0.00000 0.08831 0.10355 0.35216 0.34861 0.42526 0.72344 1.11401 1.04673 2.37310 Saccharomy 1.10187 1.12310 1.10482 1.14758 1.15097 1.13840 1.12468 1.37788 1.24852 1.29639 1.33255 1.26130 1.34704 1.33757 1.40311 1.25389 1.24951 1.19293 1.31198 1.29976 1.31247 1.28503 1.69878 0.58511 0.58507 0.59341 0.56781 0.58773 0.58885 0.58959 0.59840 0.59183 0.59118 0.59253 0.57012 0.68119 0.61258 0.48728 0.50267 0.49278 0.48987 0.48158 0.48437 0.59621 0.50823 0.49621 0.65025 0.83043 0.67613 0.52871 0.08831 0.00000 0.10393 0.32197 0.34375 0.41455 0.70490 1.14075 1.02246 2.42983 Candida_tr 1.12700 1.14262 1.14148 1.17170 1.17367 1.12846 1.12342 1.39153 1.24141 1.25800 1.29115 1.27461 1.36677 1.35717 1.41768 1.20209 1.24651 1.17782 1.30291 1.29073 1.30796 1.30400 1.75376 0.62150 0.62323 0.63400 0.61301 0.62267 0.62180 0.61772 0.60536 0.61412 0.62632 0.60662 0.59358 0.69932 0.61310 0.46491 0.48554 0.48459 0.47540 0.47294 0.45841 0.57553 0.50491 0.49037 0.63179 0.81325 0.68534 0.57553 0.10355 0.10393 0.00000 0.31856 0.33393 0.41558 0.74147 1.14004 1.05734 2.37596 Neurospora 1.06641 1.08229 1.06960 1.11758 1.08621 1.14103 1.16597 1.41617 1.27583 1.26965 1.29401 1.29241 1.29681 1.28771 1.33123 1.18987 1.31428 1.16173 1.23878 1.22732 1.27642 1.25388 1.73516 0.58837 0.59765 0.60590 0.59312 0.59943 0.58369 0.59218 0.61098 0.57907 0.59881 0.63145 0.60891 0.67500 0.60482 0.52980 0.54375 0.54558 0.54852 0.54890 0.52406 0.61971 0.50976 0.52591 0.71333 0.83323 0.71295 0.60488 0.35216 0.32197 0.31856 0.00000 0.28540 0.48848 0.75329 1.15990 1.08859 2.49267 Aspergillu 1.20615 1.21762 1.20229 1.21020 1.23050 1.33377 1.34491 1.56929 1.43300 1.41764 1.42083 1.47821 1.49690 1.48640 1.50471 1.48314 1.48529 1.33719 1.48457 1.47066 1.53518 1.49914 1.82555 0.69835 0.71596 0.72145 0.69628 0.71733 0.70379 0.71080 0.70863 0.70449 0.70998 0.69674 0.68042 0.82767 0.75332 0.63435 0.65914 0.65472 0.64199 0.65048 0.63012 0.73564 0.60260 0.66579 0.76567 0.98020 0.78338 0.72707 0.34861 0.34375 0.33393 0.28540 0.00000 0.53005 0.88105 1.30808 1.23787 2.78912 Schizosacc 1.25448 1.26064 1.22407 1.27051 1.25893 1.29699 1.25131 1.43401 1.32797 1.36369 1.37012 1.39906 1.38474 1.37502 1.42664 1.35640 1.34146 1.29357 1.52628 1.51198 1.49610 1.39637 1.85508 0.58862 0.60351 0.60061 0.58270 0.60428 0.58860 0.59490 0.59384 0.59976 0.59527 0.58014 0.56248 0.64497 0.59636 0.42791 0.44818 0.44780 0.44642 0.44236 0.47441 0.53314 0.46497 0.46082 0.63096 0.79721 0.64503 0.54575 0.42526 0.41455 0.41558 0.48848 0.53005 0.00000 0.73963 1.17895 1.13731 2.68352 Nosema_loc 1.24197 1.25430 1.24004 1.28866 1.27836 1.20457 1.27192 1.43243 1.28665 1.32966 1.35036 1.37620 1.36257 1.35300 1.41273 1.27489 1.25415 1.28811 1.51220 1.48914 1.54716 1.38657 1.85179 0.62518 0.62799 0.63694 0.63224 0.63302 0.63261 0.64575 0.66249 0.65208 0.66719 0.74311 0.70461 0.72221 0.70060 0.59583 0.60054 0.61875 0.60934 0.62261 0.58028 0.65860 0.62040 0.65946 0.79573 0.92734 0.75500 0.69542 0.72344 0.70490 0.74147 0.75329 0.88105 0.73963 0.00000 1.19716 1.34201 2.55747 Giardia_in 1.47858 1.49047 1.45737 1.39290 1.38872 1.43562 1.41461 1.65069 1.46823 1.65067 1.63865 1.58025 1.73197 1.71964 1.80783 1.60023 1.62200 1.55518 1.72429 1.69759 1.73609 1.69539 1.92760 1.05811 1.06140 1.06370 1.07662 1.06827 1.05205 1.07158 1.06465 1.07096 1.10111 1.03407 0.97696 1.05484 1.01243 1.06247 1.09103 1.08642 1.05992 1.05494 1.03624 1.15509 1.03226 1.10590 1.05678 1.10371 1.07862 1.13822 1.11401 1.14075 1.14004 1.15990 1.30808 1.17895 1.19716 0.00000 1.44860 2.86762 Deinococcu 0.86044 0.85500 0.84943 0.84934 0.83512 0.92374 0.87237 1.12934 0.98132 0.92072 0.95630 0.92838 1.10835 1.10049 1.04645 1.05987 1.04032 0.98819 1.21550 1.20441 1.09731 1.08628 1.33344 1.13545 1.13626 1.12079 1.11545 1.13034 1.11798 1.11264 1.15238 1.11385 1.14665 1.21658 1.17964 1.18834 1.17998 1.15367 1.19145 1.17707 1.13838 1.14975 1.18311 1.29238 1.16306 1.14752 1.16657 1.22799 1.11721 1.14102 1.04673 1.02246 1.05734 1.08859 1.23787 1.13731 1.34201 1.44860 0.00000 2.20577 1Treponema 1.86086 1.86191 1.81167 1.89348 1.88687 2.14490 2.22381 2.43987 2.31440 2.01325 2.15012 2.02378 2.09844 2.09372 2.05741 1.96522 2.11019 2.04503 2.24078 2.22019 2.29093 2.04599 2.49952 2.37151 2.45873 2.46203 2.44654 2.46112 2.41282 2.40501 2.46299 2.40703 2.33326 2.24359 2.16410 2.40314 2.24969 2.35148 2.32079 2.39001 2.35238 2.34730 2.35989 2.61978 2.44669 2.36999 2.45598 2.78115 2.20155 2.51694 2.37310 2.42983 2.37596 2.49267 2.78912 2.68352 2.55747 2.86762 2.20577 0.00000 Average distance (over all possible pairs of sequences): 0.95826 TREE SEARCH No tree search performed (maximum likelihood distances only). TIME STAMP Date and time: Fri Mar 01 11:43:11 2002 Runtime (excl. input) : 2436 seconds (= 40.6 minutes = 0.7 hours) Runtime (incl. input) : 2467 seconds (= 41.1 minutes = 0.7 hours)