TREE-PUZZLE 5.0 Input file name: test6-prok2.phy User tree file name: intree Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: 1st user 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: 35 sequences with 520 amino acid sites Number of constant sites: 158 (= 30.4% of all sites) Number of site patterns: 379 Number of constant site patterns: 20 (= 5.3% of all site patterns) SUBSTITUTION PROCESS Model of substitution: VT (Mueller-Vingron 2000) Amino acid frequencies (estimated from data set): pi(A) = 7.9% pi(R) = 4.6% pi(N) = 3.0% pi(D) = 5.5% pi(C) = 1.2% pi(Q) = 3.4% pi(E) = 6.6% pi(G) = 8.3% pi(H) = 1.1% pi(I) = 6.0% pi(L) = 8.9% pi(K) = 4.8% pi(M) = 3.2% pi(F) = 3.7% pi(P) = 5.1% pi(S) = 7.2% pi(T) = 5.9% pi(W) = 1.1% pi(Y) = 4.3% pi(V) = 8.3% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha: 0.63 Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0176 0.1250 2 0.1039 0.1250 3 0.2457 0.1250 4 0.4496 0.1250 5 0.7375 0.1250 6 1.1590 0.1250 7 1.8479 0.1250 8 3.4389 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 1.59. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming 1st user tree): 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 8 8 1 1 8 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 8 1 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Gossypium_ passed 99.36% Prunus_per passed 100.00% Citrus_uns passed 99.98% Brassica_n passed 99.96% Arabidopsi passed 99.98% Daucus_car passed 99.96% Vigna_radi passed 99.89% Beta_vulga passed 99.86% Mesembryan passed 99.92% Hordeum_vu passed 100.00% 1Acetabula passed 100.00% 2Acetabula passed 100.00% Scherffeli passed 99.91% Cyanidium_ passed 99.70% Bos_taurus passed 100.00% Sus_scrofa passed 100.00% 1Homo_sapi passed 100.00% A1Gallus_g passed 100.00% Fundulus_h passed 100.00% Manduca_se passed 100.00% Drosophila passed 99.98% Caenorhabd passed 99.98% Ascidia_sy passed 99.02% Trypanosom passed 99.93% Plasmodium passed 79.30% Entamoeba_ passed 99.81% Dictyostel passed 77.13% Eremotheci passed 99.15% Saccharomy passed 99.84% Candida_tr passed 99.94% Neurospora passed 81.29% Aspergillu passed 97.79% Schizosacc passed 99.90% Nosema_loc passed 79.43% Giardia_in passed 68.54% 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. 35 Gossypium_ 0.00000 0.04383 0.04120 0.03931 0.05046 0.02795 0.04083 0.05933 0.05129 0.08145 0.29237 0.29251 0.33611 0.37561 0.40236 0.40834 0.41224 0.39433 0.40761 0.40704 0.47919 0.39883 0.44967 0.46508 0.64723 0.55503 0.48186 0.60378 0.58751 0.62398 0.59067 0.70152 0.59079 0.62823 1.06582 Prunus_per 0.04383 0.00000 0.04115 0.04150 0.05186 0.03470 0.04706 0.08653 0.07265 0.08716 0.30988 0.30980 0.35681 0.39062 0.41501 0.41370 0.42010 0.40286 0.40243 0.42384 0.48984 0.40846 0.46202 0.49521 0.65843 0.54306 0.48137 0.60731 0.58752 0.62563 0.60005 0.71930 0.60562 0.63104 1.06886 Citrus_uns 0.04120 0.04115 0.00000 0.03713 0.05020 0.02402 0.03628 0.06909 0.05583 0.08593 0.31332 0.30852 0.35769 0.37323 0.41875 0.41745 0.42770 0.40896 0.41218 0.41638 0.48490 0.41920 0.46219 0.47646 0.65825 0.54587 0.49290 0.62055 0.59588 0.63649 0.60834 0.72484 0.60279 0.63989 1.07143 Brassica_n 0.03931 0.04150 0.03713 0.00000 0.01971 0.02237 0.03687 0.06071 0.05244 0.07161 0.28908 0.28621 0.34612 0.35890 0.40855 0.40723 0.41812 0.40027 0.40337 0.40885 0.48593 0.40020 0.44721 0.47853 0.65833 0.54549 0.47583 0.59965 0.57010 0.61535 0.59549 0.69930 0.58484 0.63518 1.08439 Arabidopsi 0.05046 0.05186 0.05020 0.01971 0.00000 0.04146 0.04797 0.07745 0.05932 0.07677 0.27355 0.27668 0.33572 0.37675 0.41671 0.41572 0.42635 0.40497 0.40823 0.39891 0.47792 0.39951 0.44974 0.46965 0.64505 0.55218 0.46565 0.61049 0.59005 0.62503 0.60177 0.72036 0.60640 0.63595 1.07592 Daucus_car 0.02795 0.03470 0.02402 0.02237 0.04146 0.00000 0.03007 0.05258 0.04034 0.06782 0.28835 0.28853 0.34277 0.36715 0.41015 0.40884 0.41900 0.40187 0.40241 0.40409 0.48206 0.40724 0.45062 0.47794 0.66009 0.53205 0.48369 0.61317 0.59123 0.62418 0.58592 0.70694 0.59072 0.63550 1.05949 Vigna_radi 0.04083 0.04706 0.03628 0.03687 0.04797 0.03007 0.00000 0.06023 0.04956 0.08262 0.28794 0.29422 0.32485 0.36843 0.40672 0.40540 0.41555 0.40202 0.40186 0.40005 0.48443 0.39987 0.46461 0.47956 0.66189 0.54596 0.48048 0.60729 0.59198 0.62015 0.59448 0.71391 0.59702 0.64872 1.07926 Beta_vulga 0.05933 0.08653 0.06909 0.06071 0.07745 0.05258 0.06023 0.00000 0.05881 0.10335 0.29595 0.28442 0.36320 0.37019 0.40495 0.41092 0.41589 0.40048 0.42024 0.40554 0.49431 0.40639 0.44472 0.46688 0.65854 0.57767 0.50180 0.61651 0.60094 0.60790 0.61362 0.71193 0.59611 0.66553 1.07205 Mesembryan 0.05129 0.07265 0.05583 0.05244 0.05932 0.04034 0.04956 0.05881 0.00000 0.09667 0.29179 0.28890 0.33756 0.37127 0.41474 0.41018 0.42596 0.40413 0.40492 0.40192 0.47801 0.41544 0.45265 0.47723 0.65819 0.55344 0.48198 0.61429 0.59424 0.61656 0.58131 0.70767 0.60189 0.65499 1.07866 Hordeum_vu 0.08145 0.08716 0.08593 0.07161 0.07677 0.06782 0.08262 0.10335 0.09667 0.00000 0.28948 0.29770 0.35244 0.36789 0.43464 0.43337 0.44372 0.42489 0.43255 0.43322 0.48497 0.43670 0.48051 0.48333 0.67642 0.56318 0.48888 0.61500 0.59352 0.62885 0.60104 0.71307 0.59743 0.67047 1.10906 1Acetabula 0.29237 0.30988 0.31332 0.28908 0.27355 0.28835 0.28794 0.29595 0.29179 0.28948 0.00000 0.02808 0.29588 0.39729 0.42834 0.43119 0.43703 0.43613 0.43139 0.38890 0.46070 0.41730 0.42718 0.47971 0.62572 0.52047 0.48791 0.62398 0.59451 0.60885 0.63374 0.69962 0.58185 0.74684 1.04072 2Acetabula 0.29251 0.30980 0.30852 0.28621 0.27668 0.28853 0.29422 0.28442 0.28890 0.29770 0.02808 0.00000 0.27982 0.37990 0.40732 0.41003 0.41811 0.42301 0.41694 0.37153 0.45834 0.40885 0.40419 0.44775 0.59554 0.48767 0.46103 0.60224 0.57199 0.59582 0.61102 0.68318 0.56422 0.70790 0.98295 Scherffeli 0.33611 0.35681 0.35769 0.34612 0.33572 0.34277 0.32485 0.36320 0.33756 0.35244 0.29588 0.27982 0.00000 0.44107 0.47521 0.47061 0.49467 0.47618 0.47497 0.45581 0.55493 0.45775 0.48492 0.52596 0.68579 0.56550 0.54088 0.69291 0.68403 0.70238 0.67774 0.83186 0.64721 0.72594 1.06251 Cyanidium_ 0.37561 0.39062 0.37323 0.35890 0.37675 0.36715 0.36843 0.37019 0.37127 0.36789 0.39729 0.37990 0.44107 0.00000 0.35892 0.36138 0.37635 0.37514 0.37908 0.40507 0.46563 0.36660 0.42612 0.49023 0.63125 0.50989 0.43631 0.62717 0.61482 0.61536 0.60697 0.75680 0.59825 0.70377 1.01878 Bos_taurus 0.40236 0.41501 0.41875 0.40855 0.41671 0.41015 0.40672 0.40495 0.41474 0.43464 0.42834 0.40732 0.47521 0.35892 0.00000 0.01171 0.01360 0.02977 0.06041 0.15588 0.20418 0.18696 0.20607 0.50483 0.66804 0.50003 0.39882 0.47426 0.48871 0.46624 0.53143 0.63680 0.42885 0.59846 1.06948 Sus_scrofa 0.40834 0.41370 0.41745 0.40723 0.41572 0.40884 0.40540 0.41092 0.41018 0.43337 0.43119 0.41003 0.47061 0.36138 0.01171 0.00000 0.02573 0.03831 0.06973 0.16715 0.20833 0.19371 0.21879 0.51576 0.67828 0.51388 0.40485 0.49038 0.50409 0.48686 0.54534 0.66162 0.44912 0.60316 1.09810 1Homo_sapi 0.41224 0.42010 0.42770 0.41812 0.42635 0.41900 0.41555 0.41589 0.42596 0.44372 0.43703 0.41811 0.49467 0.37635 0.01360 0.02573 0.00000 0.04014 0.06715 0.16648 0.21492 0.20251 0.22204 0.51883 0.69364 0.51623 0.40734 0.49293 0.49424 0.48597 0.54733 0.65731 0.44872 0.62148 1.09349 A1Gallus_g 0.39433 0.40286 0.40896 0.40027 0.40497 0.40187 0.40202 0.40048 0.40413 0.42489 0.43613 0.42301 0.47618 0.37514 0.02977 0.03831 0.04014 0.00000 0.06756 0.17194 0.21570 0.20323 0.22444 0.49826 0.66297 0.51575 0.39095 0.48764 0.49119 0.47656 0.55015 0.64441 0.44734 0.61196 1.06677 Fundulus_h 0.40761 0.40243 0.41218 0.40337 0.40823 0.40241 0.40186 0.42024 0.40492 0.43255 0.43139 0.41694 0.47497 0.37908 0.06041 0.06973 0.06715 0.06756 0.00000 0.15613 0.21500 0.19376 0.22163 0.53347 0.67413 0.48768 0.39510 0.48822 0.48296 0.47425 0.55050 0.65299 0.44327 0.62523 1.06179 Manduca_se 0.40704 0.42384 0.41638 0.40885 0.39891 0.40409 0.40005 0.40554 0.40192 0.43322 0.38890 0.37153 0.45581 0.40507 0.15588 0.16715 0.16648 0.17194 0.15613 0.00000 0.14239 0.20041 0.21900 0.53568 0.64487 0.49634 0.41686 0.46351 0.48558 0.45952 0.52540 0.63256 0.47545 0.58302 1.04321 Drosophila 0.47919 0.48984 0.48490 0.48593 0.47792 0.48206 0.48443 0.49431 0.47801 0.48497 0.46070 0.45834 0.55493 0.46563 0.20418 0.20833 0.21492 0.21570 0.21500 0.14239 0.00000 0.26363 0.27876 0.58163 0.72382 0.54454 0.46418 0.59684 0.59825 0.57722 0.62174 0.73904 0.53460 0.66214 1.16310 Caenorhabd 0.39883 0.40846 0.41920 0.40020 0.39951 0.40724 0.39987 0.40639 0.41544 0.43670 0.41730 0.40885 0.45775 0.36660 0.18696 0.19371 0.20251 0.20323 0.19376 0.20041 0.26363 0.00000 0.26386 0.52198 0.66014 0.51742 0.39671 0.49362 0.50979 0.50641 0.51114 0.60484 0.46609 0.62327 1.03970 Ascidia_sy 0.44967 0.46202 0.46219 0.44721 0.44974 0.45062 0.46461 0.44472 0.45265 0.48051 0.42718 0.40419 0.48492 0.42612 0.20607 0.21879 0.22204 0.22444 0.22163 0.21900 0.27876 0.26386 0.00000 0.52891 0.68113 0.58744 0.41891 0.50364 0.49751 0.49170 0.52757 0.66837 0.46218 0.66277 1.11358 Trypanosom 0.46508 0.49521 0.47646 0.47853 0.46965 0.47794 0.47956 0.46688 0.47723 0.48333 0.47971 0.44775 0.52596 0.49023 0.50483 0.51576 0.51883 0.49826 0.53347 0.53568 0.58163 0.52198 0.52891 0.00000 0.63209 0.54945 0.49662 0.66324 0.65287 0.63412 0.71618 0.76882 0.63335 0.80016 1.06395 Plasmodium 0.64723 0.65843 0.65825 0.65833 0.64505 0.66009 0.66189 0.65854 0.65819 0.67642 0.62572 0.59554 0.68579 0.63125 0.66804 0.67828 0.69364 0.66297 0.67413 0.64487 0.72382 0.66014 0.68113 0.63209 0.00000 0.68881 0.66235 0.83592 0.83520 0.81818 0.83776 0.98692 0.80165 0.93341 1.11185 Entamoeba_ 0.55503 0.54306 0.54587 0.54549 0.55218 0.53205 0.54596 0.57767 0.55344 0.56318 0.52047 0.48767 0.56550 0.50989 0.50003 0.51388 0.51623 0.51575 0.48768 0.49634 0.54454 0.51742 0.58744 0.54945 0.68881 0.00000 0.51459 0.69085 0.67912 0.68857 0.71614 0.78762 0.64768 0.75871 1.08663 Dictyostel 0.48186 0.48137 0.49290 0.47583 0.46565 0.48369 0.48048 0.50180 0.48198 0.48888 0.48791 0.46103 0.54088 0.43631 0.39882 0.40485 0.40734 0.39095 0.39510 0.41686 0.46418 0.39671 0.41891 0.49662 0.66235 0.51459 0.00000 0.55313 0.53026 0.57737 0.60693 0.73030 0.54724 0.69833 1.14623 Eremotheci 0.60378 0.60731 0.62055 0.59965 0.61049 0.61317 0.60729 0.61651 0.61429 0.61500 0.62398 0.60224 0.69291 0.62717 0.47426 0.49038 0.49293 0.48764 0.48822 0.46351 0.59684 0.49362 0.50364 0.66324 0.83592 0.69085 0.55313 0.00000 0.08825 0.10355 0.35308 0.34964 0.42656 0.72690 1.12272 Saccharomy 0.58751 0.58752 0.59588 0.57010 0.59005 0.59123 0.59198 0.60094 0.59424 0.59352 0.59451 0.57199 0.68403 0.61482 0.48871 0.50409 0.49424 0.49119 0.48296 0.48558 0.59825 0.50979 0.49751 0.65287 0.83520 0.67912 0.53026 0.08825 0.00000 0.10385 0.32282 0.34463 0.41584 0.70861 1.14987 Candida_tr 0.62398 0.62563 0.63649 0.61535 0.62503 0.62418 0.62015 0.60790 0.61656 0.62885 0.60885 0.59582 0.70238 0.61536 0.46624 0.48686 0.48597 0.47656 0.47425 0.45952 0.57722 0.50641 0.49170 0.63412 0.81818 0.68857 0.57737 0.10355 0.10385 0.00000 0.31932 0.33490 0.41671 0.74490 1.14904 Neurospora 0.59067 0.60005 0.60834 0.59549 0.60177 0.58592 0.59448 0.61362 0.58131 0.60104 0.63374 0.61102 0.67774 0.60697 0.53143 0.54534 0.54733 0.55015 0.55050 0.52540 0.62174 0.51114 0.52757 0.71618 0.83776 0.71614 0.60693 0.35308 0.32282 0.31932 0.00000 0.28606 0.49000 0.75708 1.16910 Aspergillu 0.70152 0.71930 0.72484 0.69930 0.72036 0.70694 0.71391 0.71193 0.70767 0.71307 0.69962 0.68318 0.83186 0.75680 0.63680 0.66162 0.65731 0.64441 0.65299 0.63256 0.73904 0.60484 0.66837 0.76882 0.98692 0.78762 0.73030 0.34964 0.34463 0.33490 0.28606 0.00000 0.53182 0.88610 1.31977 Schizosacc 0.59079 0.60562 0.60279 0.58484 0.60640 0.59072 0.59702 0.59611 0.60189 0.59743 0.58185 0.56422 0.64721 0.59825 0.42885 0.44912 0.44872 0.44734 0.44327 0.47545 0.53460 0.46609 0.46218 0.63335 0.80165 0.64768 0.54724 0.42656 0.41584 0.41671 0.49000 0.53182 0.00000 0.74342 1.18809 Nosema_loc 0.62823 0.63104 0.63989 0.63518 0.63595 0.63550 0.64872 0.66553 0.65499 0.67047 0.74684 0.70790 0.72594 0.70377 0.59846 0.60316 0.62148 0.61196 0.62523 0.58302 0.66214 0.62327 0.66277 0.80016 0.93341 0.75871 0.69833 0.72690 0.70861 0.74490 0.75708 0.88610 0.74342 0.00000 1.20570 Giardia_in 1.06582 1.06886 1.07143 1.08439 1.07592 1.05949 1.07926 1.07205 1.07866 1.10906 1.04072 0.98295 1.06251 1.01878 1.06948 1.09810 1.09349 1.06677 1.06179 1.04321 1.16310 1.03970 1.11358 1.06395 1.11185 1.08663 1.14623 1.12272 1.14987 1.14904 1.16910 1.31977 1.18809 1.20570 0.00000 Average distance (over all possible pairs of sequences): 0.49186 TREE SEARCH 8 tree topologies were specified by the user. MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 1 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--67 : : :-------24 Trypanosom : :-66 : : :-------------34 Nosema_loc : : :--51 : : : : :------27 Dictyostel : : : :-50 : : : : :---22 Caenorhabd : : : : :--43 : : : : : : :----23 Ascidia_sy : : : : : :-42 : : : : : : :-19 Fundulus_h : : : : : : :--39 : : : : : : : : :-18 A1Gallus_g : : : : : : : :-38 : : : : : : : : :-16 Sus_scrofa : : : : : : : :-37 : : : : : : : : :-15 Bos_taurus : : : : : : : :-36 : : : : : : : :-17 1Homo_sapi : : : : : :-41 : : : : : : :--20 Manduca_se : : : : : :--40 : : : : : :---21 Drosophila : : : :--49 : : : : :-----33 Schizosacc : : : :----48 : : : : :-30 Candida_tr : : : : :--45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :---31 Neurospora : : : :--46 : : : :----32 Aspergillu : :--65 : : :-----14 Cyanidium_ : :-64 : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02674 0.00827 36 0.00001 0.00032 Prunus_per 2 0.03029 0.00888 37 0.00874 0.00515 Citrus_uns 3 0.02128 0.00737 38 0.02217 0.00845 Brassica_n 4 0.00231 0.00243 39 0.05253 0.01339 Arabidopsi 5 0.02137 0.00718 40 0.06508 0.01528 Daucus_car 6 0.00354 0.00354 41 0.00806 0.00904 Vigna_radi 7 0.02706 0.00829 42 0.02658 0.01278 Beta_vulga 8 0.04225 0.01063 43 0.08876 0.02212 Mesembryan 9 0.03197 0.00936 44 0.03253 0.01170 Hordeum_vu 10 0.05285 0.01305 45 0.09850 0.02185 1Acetabula 11 0.03121 0.00884 46 0.09886 0.02246 2Acetabula 12 0.00173 0.00432 47 0.14482 0.02805 Scherffeli 13 0.21165 0.02988 48 0.14858 0.02816 Cyanidium_ 14 0.23125 0.03125 49 0.05761 0.02000 Bos_taurus 15 0.00001 0.00034 50 0.00362 0.01640 Sus_scrofa 16 0.01351 0.00554 51 0.06594 0.01961 1Homo_sapi 17 0.01582 0.00601 52 0.12581 0.02333 A1Gallus_g 18 0.02601 0.00817 53 0.07469 0.02024 Fundulus_h 19 0.04395 0.01132 54 0.01130 0.00613 Manduca_se 20 0.05178 0.01339 55 0.01688 0.00666 Drosophila 21 0.11995 0.01958 56 0.00785 0.00482 Caenorhabd 22 0.13138 0.02131 57 0.00504 0.00357 Ascidia_sy 23 0.18028 0.02473 58 0.00001 0.00037 Trypanosom 24 0.32803 0.04106 59 0.00388 0.00365 Plasmodium 25 0.43392 0.05291 60 0.00401 0.00396 Entamoeba_ 26 0.37376 0.04535 61 0.02407 0.01057 Dictyostel 27 0.28546 0.03635 62 0.14429 0.02504 Eremotheci 28 0.05898 0.01324 63 0.06382 0.01902 Saccharomy 29 0.04946 0.01222 64 0.03895 0.01667 Candida_tr 30 0.04192 0.01289 65 0.05400 0.02276 Neurospora 31 0.14800 0.02496 66 0.02950 0.02183 Aspergillu 32 0.17822 0.02712 67 0.07914 0.03318 Schizosacc 33 0.22550 0.03209 Nosema_loc 34 0.61232 0.06238 17 iterations until convergence Giardia_in 35 0.89073 0.09026 log L: -11539.77 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89073,Plasmodium:0.43392,(Entamoeba_:0.37376,(Trypanosom:0.32803, ((Nosema_loc:0.61232,(Dictyostel:0.28546,((Caenorhabd:0.13138,( Ascidia_sy:0.18028,((Fundulus_h:0.04395,(A1Gallus_g:0.02601,(Sus_scrofa:0.01351, (Bos_taurus:0.00001,1Homo_sapi:0.01582):0.00001):0.00874):0.02217) :0.05253,(Manduca_se:0.05178,Drosophila:0.11995):0.06508):0.00806) :0.02658):0.08876,(Schizosacc:0.22550,((Candida_tr:0.04192,(Eremotheci:0.05898, Saccharomy:0.04946):0.03253):0.09850,(Neurospora:0.14800,Aspergillu:0.17822) :0.09886):0.14482):0.14858):0.05761):0.00362):0.06594,(Cyanidium_:0.23125, ((Scherffeli:0.21165,(1Acetabula:0.03121,2Acetabula:0.00173):0.12581) :0.07469,(Hordeum_vu:0.05285,((Beta_vulga:0.04225,Mesembryan:0.03197) :0.01130,((Brassica_n:0.00231,Arabidopsi:0.02137):0.01688,(Vigna_radi:0.02706, (Gossypium_:0.02674,(Daucus_car:0.00354,(Prunus_per:0.03029,Citrus_uns:0.02128) :0.00785):0.00504):0.00001):0.00388):0.00401):0.02407):0.14429):0.06382) :0.03895):0.05400):0.02950):0.07914); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--67 : : :-------24 Trypanosom : :-66 : : :-------------34 Nosema_loc : : :--51 : : : : :------27 Dictyostel : : : :-50 : : : : :---22 Caenorhabd : : : : :--43 : : : : : : :----23 Ascidia_sy : : : : : : :-40 : : : : : : : : :-19 Fundulus_h : : : : : : : :--39 : : : : : : : : :-18 A1Gallus_g : : : : : : : :-38 : : : : : : : : :-16 Sus_scrofa : : : : : : : :-37 : : : : : : : : :-15 Bos_taurus : : : : : : : :-36 : : : : : : : :-17 1Homo_sapi : : : : : :-42 : : : : : : :--20 Manduca_se : : : : : :--41 : : : : : :---21 Drosophila : : : :--49 : : : : :-----33 Schizosacc : : : :---48 : : : : :-30 Candida_tr : : : : :--45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :---31 Neurospora : : : :--46 : : : :----32 Aspergillu : :--65 : : :-----14 Cyanidium_ : :-64 : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02671 0.00826 36 0.00001 0.00050 Prunus_per 2 0.03025 0.00886 37 0.00842 0.00511 Citrus_uns 3 0.02125 0.00736 38 0.02194 0.00842 Brassica_n 4 0.00231 0.00243 39 0.05230 0.01341 Arabidopsi 5 0.02134 0.00717 40 0.00321 0.00532 Daucus_car 6 0.00353 0.00355 41 0.06504 0.01535 Vigna_radi 7 0.02702 0.00828 42 0.02941 0.01314 Beta_vulga 8 0.04219 0.01061 43 0.09043 0.02223 Mesembryan 9 0.03193 0.00935 44 0.03258 0.01169 Hordeum_vu 10 0.05276 0.01303 45 0.09852 0.02182 1Acetabula 11 0.03114 0.00883 46 0.09850 0.02240 2Acetabula 12 0.00178 0.00436 47 0.14312 0.02786 Scherffeli 13 0.21110 0.02981 48 0.14815 0.02808 Cyanidium_ 14 0.23121 0.03122 49 0.05738 0.01994 Bos_taurus 15 0.00001 0.00098 50 0.00186 0.01651 Sus_scrofa 16 0.01349 0.00553 51 0.06615 0.01953 1Homo_sapi 17 0.01580 0.00600 52 0.12595 0.02332 A1Gallus_g 18 0.02628 0.00822 53 0.07421 0.02017 Fundulus_h 19 0.04439 0.01138 54 0.01129 0.00613 Manduca_se 20 0.05231 0.01340 55 0.01685 0.00666 Drosophila 21 0.11916 0.01947 56 0.00783 0.00481 Caenorhabd 22 0.13161 0.02132 57 0.00503 0.00357 Ascidia_sy 23 0.18366 0.02484 58 0.00001 0.00020 Trypanosom 24 0.32782 0.04102 59 0.00387 0.00365 Plasmodium 25 0.43423 0.05291 60 0.00401 0.00395 Entamoeba_ 26 0.37358 0.04533 61 0.02406 0.01056 Dictyostel 27 0.28695 0.03641 62 0.14448 0.02502 Eremotheci 28 0.05895 0.01323 63 0.06362 0.01896 Saccharomy 29 0.04939 0.01221 64 0.03839 0.01651 Candida_tr 30 0.04182 0.01287 65 0.05418 0.02267 Neurospora 31 0.14744 0.02490 66 0.02917 0.02175 Aspergillu 32 0.17841 0.02710 67 0.07883 0.03314 Schizosacc 33 0.22696 0.03214 Nosema_loc 34 0.61153 0.06231 17 iterations until convergence Giardia_in 35 0.89032 0.09030 log L: -11539.98 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89032,Plasmodium:0.43423,(Entamoeba_:0.37358,(Trypanosom:0.32782, ((Nosema_loc:0.61153,(Dictyostel:0.28695,((Caenorhabd:0.13161,( (Ascidia_sy:0.18366,(Fundulus_h:0.04439,(A1Gallus_g:0.02628,(Sus_scrofa:0.01349, (Bos_taurus:0.00001,1Homo_sapi:0.01580):0.00001):0.00842):0.02194) :0.05230):0.00321,(Manduca_se:0.05231,Drosophila:0.11916):0.06504) :0.02941):0.09043,(Schizosacc:0.22696,((Candida_tr:0.04182,(Eremotheci:0.05895, Saccharomy:0.04939):0.03258):0.09852,(Neurospora:0.14744,Aspergillu:0.17841) :0.09850):0.14312):0.14815):0.05738):0.00186):0.06615,(Cyanidium_:0.23121, ((Scherffeli:0.21110,(1Acetabula:0.03114,2Acetabula:0.00178):0.12595) :0.07421,(Hordeum_vu:0.05276,((Beta_vulga:0.04219,Mesembryan:0.03193) :0.01129,((Brassica_n:0.00231,Arabidopsi:0.02134):0.01685,(Vigna_radi:0.02702, (Gossypium_:0.02671,(Daucus_car:0.00353,(Prunus_per:0.03025,Citrus_uns:0.02125) :0.00783):0.00503):0.00001):0.00387):0.00401):0.02406):0.14448):0.06362) :0.03839):0.05418):0.02917):0.07883); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--67 : : :-------24 Trypanosom : :-66 : : :-------------34 Nosema_loc : : :--51 : : : : :------27 Dictyostel : : : :-50 : : : : :----23 Ascidia_sy : : : : :-40 : : : : : : :-19 Fundulus_h : : : : : :--39 : : : : : : :-18 A1Gallus_g : : : : : :-38 : : : : : : :-16 Sus_scrofa : : : : : :-37 : : : : : : :-15 Bos_taurus : : : : : :-36 : : : : : :-17 1Homo_sapi : : : : :---43 : : : : : : :---22 Caenorhabd : : : : : :-42 : : : : : : :--20 Manduca_se : : : : : :--41 : : : : : :---21 Drosophila : : : :--49 : : : : :-----33 Schizosacc : : : :----48 : : : : :-30 Candida_tr : : : : :--45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :---31 Neurospora : : : :---46 : : : :----32 Aspergillu : :--65 : : :-----14 Cyanidium_ : :-64 : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :-------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02656 0.00821 36 0.00001 0.00025 Prunus_per 2 0.03018 0.00884 37 0.00878 0.00511 Citrus_uns 3 0.02119 0.00734 38 0.02074 0.00811 Brassica_n 4 0.00230 0.00242 39 0.05278 0.01348 Arabidopsi 5 0.02127 0.00715 40 0.00228 0.00468 Daucus_car 6 0.00346 0.00349 41 0.05717 0.01464 Vigna_radi 7 0.02703 0.00827 42 0.01480 0.00851 Beta_vulga 8 0.04208 0.01058 43 0.10349 0.02337 Mesembryan 9 0.03180 0.00931 44 0.03271 0.01168 Hordeum_vu 10 0.05260 0.01300 45 0.09567 0.02158 1Acetabula 11 0.03210 0.00884 46 0.10091 0.02265 2Acetabula 12 0.00071 0.00406 47 0.14493 0.02808 Scherffeli 13 0.21261 0.02990 48 0.14898 0.02819 Cyanidium_ 14 0.22942 0.03110 49 0.06067 0.02041 Bos_taurus 15 0.00001 0.00025 50 0.00583 0.01621 Sus_scrofa 16 0.01346 0.00552 51 0.06508 0.01958 1Homo_sapi 17 0.01577 0.00599 52 0.12459 0.02318 A1Gallus_g 18 0.02581 0.00811 53 0.07426 0.02019 Fundulus_h 19 0.04551 0.01145 54 0.01123 0.00610 Manduca_se 20 0.05203 0.01335 55 0.01682 0.00664 Drosophila 21 0.11961 0.01952 56 0.00787 0.00481 Caenorhabd 22 0.14717 0.02172 57 0.00502 0.00356 Ascidia_sy 23 0.18205 0.02473 58 0.00001 0.00023 Trypanosom 24 0.33210 0.04142 59 0.00389 0.00365 Plasmodium 25 0.43477 0.05298 60 0.00400 0.00394 Entamoeba_ 26 0.37239 0.04523 61 0.02387 0.01054 Dictyostel 27 0.28888 0.03665 62 0.14499 0.02503 Eremotheci 28 0.05863 0.01316 63 0.06351 0.01900 Saccharomy 29 0.04939 0.01217 64 0.04096 0.01701 Candida_tr 30 0.04132 0.01278 65 0.05128 0.02269 Neurospora 31 0.14797 0.02493 66 0.02787 0.02136 Aspergillu 32 0.17763 0.02705 67 0.07906 0.03316 Schizosacc 33 0.22551 0.03207 Nosema_loc 34 0.60430 0.06196 16 iterations until convergence Giardia_in 35 0.89092 0.09052 log L: -11540.85 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89092,Plasmodium:0.43477,(Entamoeba_:0.37239,(Trypanosom:0.33210, ((Nosema_loc:0.60430,(Dictyostel:0.28888,(((Ascidia_sy:0.18205, (Fundulus_h:0.04551,(A1Gallus_g:0.02581,(Sus_scrofa:0.01346,(Bos_taurus:0.00001, 1Homo_sapi:0.01577):0.00001):0.00878):0.02074):0.05278):0.00228,( Caenorhabd:0.14717,(Manduca_se:0.05203,Drosophila:0.11961):0.05717) :0.01480):0.10349,(Schizosacc:0.22551,((Candida_tr:0.04132,(Eremotheci:0.05863, Saccharomy:0.04939):0.03271):0.09567,(Neurospora:0.14797,Aspergillu:0.17763) :0.10091):0.14493):0.14898):0.06067):0.00583):0.06508,(Cyanidium_:0.22942, ((Scherffeli:0.21261,(1Acetabula:0.03210,2Acetabula:0.00071):0.12459) :0.07426,(Hordeum_vu:0.05260,((Beta_vulga:0.04208,Mesembryan:0.03180) :0.01123,((Brassica_n:0.00230,Arabidopsi:0.02127):0.01682,(Vigna_radi:0.02703, (Gossypium_:0.02656,(Daucus_car:0.00346,(Prunus_per:0.03018,Citrus_uns:0.02119) :0.00787):0.00502):0.00001):0.00389):0.00400):0.02387):0.14499):0.06351) :0.04096):0.05128):0.02787):0.07906); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--67 : : :-------24 Trypanosom : :-66 : : :------27 Dictyostel : : :--51 : : : : :----23 Ascidia_sy : : : : :-40 : : : : : : :-19 Fundulus_h : : : : : :--39 : : : : : : :-18 A1Gallus_g : : : : : :-38 : : : : : : :-16 Sus_scrofa : : : : : :-37 : : : : : : :-15 Bos_taurus : : : : : :-36 : : : : : :-17 1Homo_sapi : : : : :---43 : : : : : : :---22 Caenorhabd : : : : : :-42 : : : : : : :--20 Manduca_se : : : : : :--41 : : : : : :---21 Drosophila : : : :--50 : : : : :------------34 Nosema_loc : : : :--49 : : : : :-----33 Schizosacc : : : :--48 : : : : :-30 Candida_tr : : : : :--45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :----31 Neurospora : : : :--46 : : : :----32 Aspergillu : :--65 : : :-----14 Cyanidium_ : :-64 : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :-------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02667 0.00824 36 0.00001 0.00112 Prunus_per 2 0.03026 0.00887 37 0.00889 0.00514 Citrus_uns 3 0.02126 0.00736 38 0.02057 0.00815 Brassica_n 4 0.00231 0.00243 39 0.05315 0.01364 Arabidopsi 5 0.02133 0.00717 40 0.00166 0.00479 Daucus_car 6 0.00347 0.00351 41 0.05743 0.01475 Vigna_radi 7 0.02710 0.00829 42 0.01550 0.00883 Beta_vulga 8 0.04223 0.01062 43 0.11374 0.02421 Mesembryan 9 0.03192 0.00934 44 0.03115 0.01151 Hordeum_vu 10 0.05253 0.01299 45 0.09881 0.02180 1Acetabula 11 0.03193 0.00887 46 0.09660 0.02222 2Acetabula 12 0.00099 0.00408 47 0.14589 0.02788 Scherffeli 13 0.21388 0.03010 48 0.08176 0.02438 Cyanidium_ 14 0.22828 0.03114 49 0.07603 0.02217 Bos_taurus 15 0.00001 0.00040 50 0.05462 0.01932 Sus_scrofa 16 0.01351 0.00554 51 0.06117 0.01916 1Homo_sapi 17 0.01582 0.00601 52 0.12472 0.02329 A1Gallus_g 18 0.02583 0.00813 53 0.07423 0.02026 Fundulus_h 19 0.04587 0.01153 54 0.01121 0.00612 Manduca_se 20 0.05230 0.01342 55 0.01686 0.00666 Drosophila 21 0.11991 0.01958 56 0.00788 0.00482 Caenorhabd 22 0.14779 0.02185 57 0.00504 0.00357 Ascidia_sy 23 0.18327 0.02492 58 0.00001 0.00024 Trypanosom 24 0.33476 0.04160 59 0.00389 0.00366 Plasmodium 25 0.43584 0.05314 60 0.00404 0.00398 Entamoeba_ 26 0.37399 0.04531 61 0.02416 0.01055 Dictyostel 27 0.28086 0.03592 62 0.14628 0.02527 Eremotheci 28 0.05928 0.01327 63 0.06805 0.01975 Saccharomy 29 0.04916 0.01220 64 0.04402 0.01735 Candida_tr 30 0.04350 0.01299 65 0.04961 0.02210 Neurospora 31 0.14938 0.02491 66 0.02722 0.02129 Aspergillu 32 0.17728 0.02698 67 0.08027 0.03340 Schizosacc 33 0.22528 0.03203 Nosema_loc 34 0.56123 0.05951 16 iterations until convergence Giardia_in 35 0.89877 0.09143 log L: -11527.28 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89877,Plasmodium:0.43584,(Entamoeba_:0.37399,(Trypanosom:0.33476, ((Dictyostel:0.28086,(((Ascidia_sy:0.18327,(Fundulus_h:0.04587, (A1Gallus_g:0.02583,(Sus_scrofa:0.01351,(Bos_taurus:0.00001,1Homo_sapi:0.01582) :0.00001):0.00889):0.02057):0.05315):0.00166,(Caenorhabd:0.14779,( Manduca_se:0.05230,Drosophila:0.11991):0.05743):0.01550):0.11374, (Nosema_loc:0.56123,(Schizosacc:0.22528,((Candida_tr:0.04350,(Eremotheci:0.05928, Saccharomy:0.04916):0.03115):0.09881,(Neurospora:0.14938,Aspergillu:0.17728) :0.09660):0.14589):0.08176):0.07603):0.05462):0.06117,(Cyanidium_:0.22828, ((Scherffeli:0.21388,(1Acetabula:0.03193,2Acetabula:0.00099):0.12472) :0.07423,(Hordeum_vu:0.05253,((Beta_vulga:0.04223,Mesembryan:0.03192) :0.01121,((Brassica_n:0.00231,Arabidopsi:0.02133):0.01686,(Vigna_radi:0.02710, (Gossypium_:0.02667,(Daucus_car:0.00347,(Prunus_per:0.03026,Citrus_uns:0.02126) :0.00788):0.00504):0.00001):0.00389):0.00404):0.02416):0.14628):0.06805) :0.04402):0.04961):0.02722):0.08027); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 5 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--67 : : :-------24 Trypanosom : :-66 : : :-----14 Cyanidium_ : :--65 : : :------27 Dictyostel : : :--51 : : : : :----23 Ascidia_sy : : : : :-40 : : : : : : :-19 Fundulus_h : : : : : :--39 : : : : : : :-18 A1Gallus_g : : : : : :-38 : : : : : : :-16 Sus_scrofa : : : : : :-37 : : : : : : :-15 Bos_taurus : : : : : :-36 : : : : : :-17 1Homo_sapi : : : : :---43 : : : : : : :---22 Caenorhabd : : : : : :-42 : : : : : : :--20 Manduca_se : : : : : :--41 : : : : : :---21 Drosophila : : : :--50 : : : : :------------34 Nosema_loc : : : :--49 : : : : :-----33 Schizosacc : : : :--48 : : : : :-30 Candida_tr : : : : :---45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :----31 Neurospora : : : :--46 : : : :----32 Aspergillu : :-64 : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :-------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02659 0.00822 36 0.00001 0.00112 Prunus_per 2 0.03020 0.00885 37 0.00885 0.00513 Citrus_uns 3 0.02121 0.00735 38 0.02058 0.00813 Brassica_n 4 0.00230 0.00242 39 0.05262 0.01351 Arabidopsi 5 0.02128 0.00715 40 0.00219 0.00498 Daucus_car 6 0.00344 0.00348 41 0.05744 0.01468 Vigna_radi 7 0.02706 0.00827 42 0.01532 0.00874 Beta_vulga 8 0.04214 0.01059 43 0.10926 0.02359 Mesembryan 9 0.03183 0.00932 44 0.03164 0.01150 Hordeum_vu 10 0.05254 0.01297 45 0.09961 0.02180 1Acetabula 11 0.03197 0.00884 46 0.09500 0.02199 2Acetabula 12 0.00085 0.00415 47 0.14569 0.02786 Scherffeli 13 0.21243 0.02997 48 0.08403 0.02449 Cyanidium_ 14 0.24205 0.03213 49 0.07613 0.02204 Bos_taurus 15 0.00001 0.00040 50 0.05207 0.01911 Sus_scrofa 16 0.01347 0.00552 51 0.07955 0.02120 1Homo_sapi 17 0.01577 0.00599 52 0.12439 0.02325 A1Gallus_g 18 0.02576 0.00810 53 0.07382 0.02002 Fundulus_h 19 0.04564 0.01148 54 0.01117 0.00611 Manduca_se 20 0.05176 0.01335 55 0.01683 0.00664 Drosophila 21 0.11990 0.01955 56 0.00787 0.00481 Caenorhabd 22 0.14665 0.02169 57 0.00503 0.00356 Ascidia_sy 23 0.18309 0.02484 58 0.00001 0.00033 Trypanosom 24 0.32933 0.04115 59 0.00389 0.00366 Plasmodium 25 0.42870 0.05246 60 0.00405 0.00398 Entamoeba_ 26 0.37300 0.04521 61 0.02383 0.01047 Dictyostel 27 0.28625 0.03611 62 0.14521 0.02510 Eremotheci 28 0.05901 0.01322 63 0.08287 0.02146 Saccharomy 29 0.04904 0.01217 64 0.00154 0.01015 Candida_tr 30 0.04277 0.01288 65 0.06338 0.02376 Neurospora 31 0.14886 0.02479 66 0.03091 0.02169 Aspergillu 32 0.17631 0.02681 67 0.07805 0.03300 Schizosacc 33 0.22391 0.03188 Nosema_loc 34 0.55725 0.05913 16 iterations until convergence Giardia_in 35 0.89612 0.09114 log L: -11534.91 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89612,Plasmodium:0.42870,(Entamoeba_:0.37300,(Trypanosom:0.32933, (Cyanidium_:0.24205,((Dictyostel:0.28625,(((Ascidia_sy:0.18309, (Fundulus_h:0.04564,(A1Gallus_g:0.02576,(Sus_scrofa:0.01347,(Bos_taurus:0.00001, 1Homo_sapi:0.01577):0.00001):0.00885):0.02058):0.05262):0.00219,( Caenorhabd:0.14665,(Manduca_se:0.05176,Drosophila:0.11990):0.05744) :0.01532):0.10926,(Nosema_loc:0.55725,(Schizosacc:0.22391,((Candida_tr:0.04277, (Eremotheci:0.05901,Saccharomy:0.04904):0.03164):0.09961,(Neurospora:0.14886, Aspergillu:0.17631):0.09500):0.14569):0.08403):0.07613):0.05207):0.07955, ((Scherffeli:0.21243,(1Acetabula:0.03197,2Acetabula:0.00085):0.12439) :0.07382,(Hordeum_vu:0.05254,((Beta_vulga:0.04214,Mesembryan:0.03183) :0.01117,((Brassica_n:0.00230,Arabidopsi:0.02128):0.01683,(Vigna_radi:0.02706, (Gossypium_:0.02659,(Daucus_car:0.00344,(Prunus_per:0.03020,Citrus_uns:0.02121) :0.00787):0.00503):0.00001):0.00389):0.00405):0.02383):0.14521):0.08287) :0.00154):0.06338):0.03091):0.07805); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 6 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--66 : : :-------24 Trypanosom : :-65 : : :------27 Dictyostel : : :--51 : : : : :----23 Ascidia_sy : : : : :-40 : : : : : : :-19 Fundulus_h : : : : : :--39 : : : : : : :-18 A1Gallus_g : : : : : :-38 : : : : : : :-16 Sus_scrofa : : : : : :-37 : : : : : : :-15 Bos_taurus : : : : : :-36 : : : : : :-17 1Homo_sapi : : : : :---43 : : : : : : :---22 Caenorhabd : : : : : :-42 : : : : : : :--20 Manduca_se : : : : : :--41 : : : : : :---21 Drosophila : : : :--50 : : : : :------------34 Nosema_loc : : : :--49 : : : : :-----33 Schizosacc : : : :--48 : : : : :-30 Candida_tr : : : : :---45 : : : : : : :--28 Eremotheci : : : : : :-44 : : : : : :-29 Saccharomy : : : :---47 : : : : :----31 Neurospora : : : :--46 : : : :----32 Aspergillu : :--64 : :-----14 Cyanidium_ : : : : :-----13 Scherffeli : : :--53 : : : : :-11 1Acetabula : : : :---52 : : : :-12 2Acetabula : :--63 : : :--10 Hordeum_vu : :---62 : : :-8 Beta_vulga : : :-54 : : : :-9 Mesembryan : :-61 : : :-4 Brassica_n : : :-55 : : : :-5 Arabidopsi : :-60 : : :-7 Vigna_radi : :-59 : : :-1 Gossypium_ : :-58 : : :-6 Daucus_car : :-57 : : :-2 Prunus_per : :-56 : :-3 Citrus_uns : :-------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02659 0.00822 36 0.00001 0.00046 Prunus_per 2 0.03020 0.00885 37 0.00885 0.00513 Citrus_uns 3 0.02121 0.00735 38 0.02058 0.00813 Brassica_n 4 0.00230 0.00242 39 0.05262 0.01351 Arabidopsi 5 0.02128 0.00715 40 0.00219 0.00497 Daucus_car 6 0.00344 0.00348 41 0.05745 0.01468 Vigna_radi 7 0.02706 0.00827 42 0.01532 0.00874 Beta_vulga 8 0.04215 0.01059 43 0.10920 0.02358 Mesembryan 9 0.03183 0.00932 44 0.03164 0.01150 Hordeum_vu 10 0.05252 0.01297 45 0.09961 0.02180 1Acetabula 11 0.03198 0.00884 46 0.09502 0.02199 2Acetabula 12 0.00084 0.00422 47 0.14572 0.02786 Scherffeli 13 0.21247 0.02997 48 0.08404 0.02448 Cyanidium_ 14 0.24310 0.03214 49 0.07615 0.02204 Bos_taurus 15 0.00001 0.00037 50 0.05214 0.01912 Sus_scrofa 16 0.01347 0.00552 51 0.07984 0.02122 1Homo_sapi 17 0.01577 0.00599 52 0.12436 0.02325 A1Gallus_g 18 0.02576 0.00810 53 0.07380 0.02002 Fundulus_h 19 0.04564 0.01148 54 0.01117 0.00611 Manduca_se 20 0.05177 0.01335 55 0.01683 0.00664 Drosophila 21 0.11989 0.01955 56 0.00787 0.00481 Caenorhabd 22 0.14666 0.02169 57 0.00503 0.00356 Ascidia_sy 23 0.18310 0.02484 58 0.00001 0.00030 Trypanosom 24 0.32936 0.04115 59 0.00389 0.00366 Plasmodium 25 0.42892 0.05246 60 0.00405 0.00398 Entamoeba_ 26 0.37339 0.04524 61 0.02385 0.01047 Dictyostel 27 0.28622 0.03611 62 0.14522 0.02510 Eremotheci 28 0.05901 0.01322 63 0.08307 0.02148 Saccharomy 29 0.04905 0.01217 64 0.06413 0.02380 Candida_tr 30 0.04277 0.01288 65 0.03089 0.02171 Neurospora 31 0.14887 0.02480 66 0.07770 0.03294 Aspergillu 32 0.17631 0.02681 Schizosacc 33 0.22390 0.03188 Nosema_loc 34 0.55730 0.05914 16 iterations until convergence Giardia_in 35 0.89647 0.09117 log L: -11534.92 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.89647,Plasmodium:0.42892,(Entamoeba_:0.37339,(Trypanosom:0.32936, ((Dictyostel:0.28622,(((Ascidia_sy:0.18310,(Fundulus_h:0.04564, (A1Gallus_g:0.02576,(Sus_scrofa:0.01347,(Bos_taurus:0.00001,1Homo_sapi:0.01577) :0.00001):0.00885):0.02058):0.05262):0.00219,(Caenorhabd:0.14666,( Manduca_se:0.05177,Drosophila:0.11989):0.05745):0.01532):0.10920, (Nosema_loc:0.55730,(Schizosacc:0.22390,((Candida_tr:0.04277,(Eremotheci:0.05901, Saccharomy:0.04905):0.03164):0.09961,(Neurospora:0.14887,Aspergillu:0.17631) :0.09502):0.14572):0.08404):0.07615):0.05214):0.07984,Cyanidium_:0.24310, ((Scherffeli:0.21247,(1Acetabula:0.03198,2Acetabula:0.00084):0.12436) :0.07380,(Hordeum_vu:0.05252,((Beta_vulga:0.04215,Mesembryan:0.03183) :0.01117,((Brassica_n:0.00230,Arabidopsi:0.02128):0.01683,(Vigna_radi:0.02706, (Gossypium_:0.02659,(Daucus_car:0.00344,(Prunus_per:0.03020,Citrus_uns:0.02121) :0.00787):0.00503):0.00001):0.00389):0.00405):0.02385):0.14522):0.08307) :0.06413):0.03089):0.07770); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 7 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------25 Plasmodium : : :--------26 Entamoeba_ :--65 : : :-------24 Trypanosom : :-64 : : :------14 Cyanidium_ : : : : :-------27 Dictyostel : --63 : : :----23 Ascidia_sy : : :-40 : : : : :-19 Fundulus_h : : : :--39 : : : : :-18 A1Gallus_g : : : :-38 : : : : :-16 Sus_scrofa : : : :-37 : : : : :-15 Bos_taurus : : : :-36 : : : :-17 1Homo_sapi : : :---43 : : : : :---22 Caenorhabd : : : :-42 : : : : :--20 Manduca_se : : : :--41 : : : :---21 Drosophila : :---50 : : : :------------34 Nosema_loc : : :--49 : : : :-----33 Schizosacc : : :--48 : : : :-30 Candida_tr : : : :---45 : : : : : :--28 Eremotheci : : : : :-44 : : : : :-29 Saccharomy : : :---47 : : : :----31 Neurospora : : :--46 : : :----32 Aspergillu : : : : :-----13 Scherffeli : : :--52 : : : : :-11 1Acetabula : : : :---51 : : : :-12 2Acetabula : :---62 : : :--10 Hordeum_vu : :---61 : : :-8 Beta_vulga : : :-53 : : : :-9 Mesembryan : :-60 : : :-4 Brassica_n : : :-54 : : : :-5 Arabidopsi : :-59 : : :-7 Vigna_radi : :-58 : : :-1 Gossypium_ : :-57 : : :-6 Daucus_car : :-56 : : :-2 Prunus_per : :-55 : :-3 Citrus_uns : :-------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02656 0.00821 36 0.00001 0.00034 Prunus_per 2 0.03024 0.00885 37 0.00870 0.00510 Citrus_uns 3 0.02121 0.00735 38 0.01939 0.00789 Brassica_n 4 0.00231 0.00242 39 0.05047 0.01336 Arabidopsi 5 0.02129 0.00716 40 0.00001 0.00028 Daucus_car 6 0.00342 0.00346 41 0.05945 0.01492 Vigna_radi 7 0.02710 0.00828 42 0.01674 0.00894 Beta_vulga 8 0.04219 0.01060 43 0.11389 0.02390 Mesembryan 9 0.03180 0.00931 44 0.03259 0.01163 Hordeum_vu 10 0.05248 0.01299 45 0.10052 0.02186 1Acetabula 11 0.03172 0.00885 46 0.09381 0.02180 2Acetabula 12 0.00117 0.00413 47 0.14601 0.02786 Scherffeli 13 0.21420 0.03025 48 0.08239 0.02421 Cyanidium_ 14 0.26261 0.03350 49 0.07932 0.02238 Bos_taurus 15 0.00001 0.00044 50 0.09923 0.02341 Sus_scrofa 16 0.01352 0.00554 51 0.12277 0.02340 1Homo_sapi 17 0.01584 0.00602 52 0.07447 0.02023 A1Gallus_g 18 0.02606 0.00816 53 0.01122 0.00611 Fundulus_h 19 0.04734 0.01166 54 0.01685 0.00664 Manduca_se 20 0.05244 0.01348 55 0.00789 0.00481 Drosophila 21 0.11991 0.01960 56 0.00503 0.00356 Caenorhabd 22 0.14574 0.02165 57 0.00001 0.00021 Ascidia_sy 23 0.18599 0.02508 58 0.00391 0.00366 Trypanosom 24 0.34036 0.04192 59 0.00397 0.00392 Plasmodium 25 0.43827 0.05365 60 0.02400 0.01053 Entamoeba_ 26 0.36790 0.04480 61 0.14607 0.02537 Dictyostel 27 0.33024 0.03894 62 0.10529 0.02349 Eremotheci 28 0.05957 0.01332 63 0.06200 0.02330 Saccharomy 29 0.04897 0.01220 64 0.03007 0.02186 Candida_tr 30 0.04232 0.01290 65 0.08428 0.03420 Neurospora 31 0.15018 0.02494 Aspergillu 32 0.17602 0.02685 Schizosacc 33 0.22325 0.03183 Nosema_loc 34 0.55673 0.05888 16 iterations until convergence Giardia_in 35 0.90071 0.09176 log L: -11553.24 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:0.90071,Plasmodium:0.43827,(Entamoeba_:0.36790,(Trypanosom:0.34036, (Cyanidium_:0.26261,Dictyostel:0.33024,(((Ascidia_sy:0.18599,(Fundulus_h:0.04734, (A1Gallus_g:0.02606,(Sus_scrofa:0.01352,(Bos_taurus:0.00001,1Homo_sapi:0.01584) :0.00001):0.00870):0.01939):0.05047):0.00001,(Caenorhabd:0.14574,( Manduca_se:0.05244,Drosophila:0.11991):0.05945):0.01674):0.11389, (Nosema_loc:0.55673,(Schizosacc:0.22325,((Candida_tr:0.04232,(Eremotheci:0.05957, Saccharomy:0.04897):0.03259):0.10052,(Neurospora:0.15018,Aspergillu:0.17602) :0.09381):0.14601):0.08239):0.07932):0.09923,((Scherffeli:0.21420, (1Acetabula:0.03172,2Acetabula:0.00117):0.12277):0.07447,(Hordeum_vu:0.05248, ((Beta_vulga:0.04219,Mesembryan:0.03180):0.01122,((Brassica_n:0.00231, Arabidopsi:0.02129):0.01685,(Vigna_radi:0.02710,(Gossypium_:0.02656, (Daucus_car:0.00342,(Prunus_per:0.03024,Citrus_uns:0.02121):0.00789) :0.00503):0.00001):0.00391):0.00397):0.02400):0.14607):0.10529):0.06200) :0.03007):0.08428); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 8 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :------------25 Plasmodium : :---------26 Entamoeba_ : :---------24 Trypanosom : :------14 Cyanidium_ : :-------27 Dictyostel : : :----23 Ascidia_sy : :-40 : : : :-19 Fundulus_h : : :--39 : : : :-18 A1Gallus_g : : :-38 : : : :-16 Sus_scrofa : : :-37 : : : :-15 Bos_taurus : : :-36 : : :-17 1Homo_sapi : :---43 : : : :---22 Caenorhabd : : :-42 : : : :--20 Manduca_se : : :--41 : : :---21 Drosophila :---50 : : :------------34 Nosema_loc : :--49 : : :-----33 Schizosacc : :--48 : : :-30 Candida_tr : : :--45 : : : : :--28 Eremotheci : : : :-44 : : : :-29 Saccharomy : :---47 : : :----31 Neurospora : :--46 : :----32 Aspergillu : : :-----13 Scherffeli : :--52 : : : :-11 1Acetabula : : :---51 : : :-12 2Acetabula :---62 : : :--10 Hordeum_vu : :----61 : : :-8 Beta_vulga : : :-53 : : : :-9 Mesembryan : :-60 : : :-4 Brassica_n : : :-54 : : : :-5 Arabidopsi : :-59 : : :-7 Vigna_radi : :-58 : : :-1 Gossypium_ : :-57 : : :-6 Daucus_car : :-56 : : :-2 Prunus_per : :-55 : :-3 Citrus_uns : :----------------------35 Giardia_in branch length S.E. branch length S.E. Gossypium_ 1 0.02654 0.00821 36 0.00001 9.00000 Prunus_per 2 0.03028 0.00886 37 0.00874 0.00512 Citrus_uns 3 0.02122 0.00735 38 0.01941 0.00791 Brassica_n 4 0.00231 0.00242 39 0.04981 0.01331 Arabidopsi 5 0.02130 0.00716 40 0.00001 0.00083 Daucus_car 6 0.00339 0.00345 41 0.05951 0.01499 Vigna_radi 7 0.02713 0.00828 42 0.01709 0.00905 Beta_vulga 8 0.04224 0.01060 43 0.11354 0.02402 Mesembryan 9 0.03178 0.00931 44 0.03251 0.01167 Hordeum_vu 10 0.05236 0.01300 45 0.09861 0.02186 1Acetabula 11 0.03194 0.00886 46 0.09627 0.02216 2Acetabula 12 0.00096 0.00418 47 0.14757 0.02813 Scherffeli 13 0.21594 0.03048 48 0.08245 0.02443 Cyanidium_ 14 0.26979 0.03404 49 0.08082 0.02279 Bos_taurus 15 0.00001 9.00000 50 0.10362 0.02377 Sus_scrofa 16 0.01357 0.00557 51 0.12249 0.02344 1Homo_sapi 17 0.01590 0.00604 52 0.07155 0.01989 A1Gallus_g 18 0.02616 0.00819 53 0.01122 0.00611 Fundulus_h 19 0.04762 0.01171 54 0.01685 0.00664 Manduca_se 20 0.05322 0.01359 55 0.00790 0.00482 Drosophila 21 0.11982 0.01963 56 0.00504 0.00357 Caenorhabd 22 0.14707 0.02179 57 0.00001 0.00028 Ascidia_sy 23 0.18674 0.02518 58 0.00391 0.00366 Trypanosom 24 0.40126 0.04426 59 0.00398 0.00394 Plasmodium 25 0.57753 0.05761 60 0.02413 0.01059 Entamoeba_ 26 0.44013 0.04730 61 0.15078 0.02579 Dictyostel 27 0.32824 0.03880 62 0.11244 0.02417 Eremotheci 28 0.05978 0.01336 Saccharomy 29 0.04919 0.01224 Candida_tr 30 0.04259 0.01296 Neurospora 31 0.15158 0.02515 Aspergillu 32 0.17660 0.02699 Schizosacc 33 0.22538 0.03215 Nosema_loc 34 0.56446 0.05975 18 iterations until convergence Giardia_in 35 1.05346 0.09864 log L: -11570.30 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia_in:1.05346,Plasmodium:0.57753,Entamoeba_:0.44013,Trypanosom:0.40126, Cyanidium_:0.26979,Dictyostel:0.32824,(((Ascidia_sy:0.18674,(Fundulus_h:0.04762, (A1Gallus_g:0.02616,(Sus_scrofa:0.01357,(Bos_taurus:0.00001,1Homo_sapi:0.01590) :0.00001):0.00874):0.01941):0.04981):0.00001,(Caenorhabd:0.14707,( Manduca_se:0.05322,Drosophila:0.11982):0.05951):0.01709):0.11354, (Nosema_loc:0.56446,(Schizosacc:0.22538,((Candida_tr:0.04259,(Eremotheci:0.05978, Saccharomy:0.04919):0.03251):0.09861,(Neurospora:0.15158,Aspergillu:0.17660) :0.09627):0.14757):0.08245):0.08082):0.10362,((Scherffeli:0.21594, (1Acetabula:0.03194,2Acetabula:0.00096):0.12249):0.07155,(Hordeum_vu:0.05236, ((Beta_vulga:0.04224,Mesembryan:0.03178):0.01122,((Brassica_n:0.00231, Arabidopsi:0.02130):0.01685,(Vigna_radi:0.02713,(Gossypium_:0.02654, (Daucus_car:0.00339,(Prunus_per:0.03028,Citrus_uns:0.02122):0.00790) :0.00504):0.00001):0.00391):0.00398):0.02413):0.15078):0.11244); COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. Significantly worse -------------------------------------------------------- 1 -11539.77 12.48 11.35 no 2 -11539.98 12.70 11.21 no 3 -11540.85 13.57 9.80 no 4 -11527.28 0.00 <----------------- best tree 5 -11534.91 7.63 5.12 no 6 -11534.92 7.64 5.10 no 7 -11553.24 25.96 9.15 yes 8 -11570.30 43.02 11.31 yes This test (5% significance) follows Kishino and Hasegawa (1989). TIME STAMP Date and time: Fri Mar 01 13:14:10 2002 Runtime (excl. input) : 6445 seconds (= 107.4 minutes = 1.8 hours) Runtime (incl. input) : 6508 seconds (= 108.5 minutes = 1.8 hours)