TREE-PUZZLE 5.0 Input file name: infile 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: 36 sequences with 698 amino acid sites Number of constant sites: 80 (= 11.5% of all sites) Number of site patterns: 597 Number of constant site patterns: 18 (= 3.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: VT (Mueller-Vingron 2000) Amino acid frequencies (estimated from data set): pi(A) = 7.3% pi(R) = 5.2% pi(N) = 3.0% pi(D) = 5.7% pi(C) = 0.9% pi(Q) = 3.5% pi(E) = 8.0% pi(G) = 8.4% pi(H) = 1.1% pi(I) = 6.3% pi(L) = 8.1% pi(K) = 5.4% pi(M) = 3.1% pi(F) = 3.4% pi(P) = 5.3% pi(S) = 6.4% pi(T) = 5.7% pi(W) = 1.2% pi(Y) = 3.7% pi(V) = 8.2% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha: 0.60 Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0146 0.1250 2 0.0938 0.1250 3 0.2304 0.1250 4 0.4318 0.1250 5 0.7208 0.1250 6 1.1492 0.1250 7 1.8561 0.1250 8 3.5033 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 1.67. 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 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 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 1 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 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 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 BMethanos passed 99.80% MMethanos passed 96.87% Archaeogl passed 5.81% Haloferax failed 0.31% Halobact failed 0.09% jMethanoco passed 30.75% Methanobac passed 31.67% Desulfuroc passed 22.60% Thermococ passed 15.45% Enterococ passed 12.20% Sulfolobus passed 33.61% Daucus passed 95.32% Gossypium passed 88.83% Arabidopsi passed 92.73% '1Acetab' passed 99.95% '2Acetab' passed 99.74% Cyanidium passed 99.68% Trypanos passed 98.24% Homo passed 99.33% Bos passed 99.81% Mus passed 99.34% Gallus passed 99.95% Manduca passed 99.74% Aedes passed 99.84% Drosophila passed 99.18% Dictyost passed 39.00% Entamoeba passed 99.01% Saccharom passed 90.80% Candida passed 94.47% Neurosp passed 90.19% Schizosac passed 50.12% Plasmodium passed 33.80% Giardia failed 3.70% Thermus passed 18.87% Deinococ passed 37.05% Borrelia passed 33.63% 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. 36 BMethanos 0.00000 0.15835 0.61165 0.75284 0.73621 0.85550 0.87714 0.79838 0.80427 1.13945 1.32094 1.45077 1.41267 1.48362 1.46987 1.55851 1.27098 1.43792 1.54721 1.49961 1.54201 1.52137 1.45151 1.65462 1.55585 1.47664 1.32630 1.56052 1.49106 1.50062 1.61274 1.68136 2.09975 0.96853 1.10582 2.38562 MMethanos 0.15835 0.00000 0.63487 0.77554 0.80844 0.90184 0.92701 0.83616 0.83612 1.10096 1.34417 1.44349 1.40969 1.48131 1.45741 1.53448 1.32609 1.50226 1.56970 1.51923 1.54718 1.54058 1.45602 1.69226 1.58784 1.53923 1.39396 1.60536 1.54127 1.56201 1.64585 1.68095 2.05864 1.02372 1.17355 2.58526 Archaeogl 0.61165 0.63487 0.00000 0.81398 0.89403 0.70823 0.77431 0.65147 0.64710 1.04169 1.07460 1.47308 1.43681 1.50349 1.40977 1.44718 1.36328 1.58365 1.63538 1.57768 1.60460 1.58438 1.45435 1.63879 1.54195 1.52754 1.39703 1.48176 1.48169 1.54017 1.65209 1.61336 2.01894 0.94229 1.09850 2.46322 Haloferax 0.75284 0.77554 0.81398 0.00000 0.24007 0.91052 0.88788 0.90042 0.89933 1.12885 1.38360 1.57455 1.57503 1.63191 1.49153 1.53083 1.39957 1.60295 1.48524 1.46530 1.49029 1.49392 1.55686 1.74873 1.63964 1.62264 1.43029 1.73008 1.71820 1.59548 1.71581 1.86248 2.27823 1.03173 1.18896 2.38620 Halobact 0.73621 0.80844 0.89403 0.24007 0.00000 0.96735 0.94297 0.94264 0.94396 1.13370 1.39023 1.61288 1.63247 1.65958 1.46540 1.51995 1.42304 1.60960 1.57161 1.54769 1.56574 1.55291 1.52229 1.73916 1.67852 1.70049 1.41850 1.65057 1.65217 1.50563 1.62345 1.85222 2.18002 1.13912 1.25195 2.54292 jMethanoco 0.85550 0.90184 0.70823 0.91052 0.96735 0.00000 0.50799 0.57542 0.58274 0.92882 1.08937 1.41412 1.41286 1.43417 1.36217 1.41766 1.22359 1.42966 1.44906 1.41678 1.42237 1.43233 1.34313 1.56181 1.45083 1.43028 1.37383 1.42445 1.39188 1.34593 1.57470 1.68472 1.97596 0.89752 1.08375 2.31125 Methanobac 0.87714 0.92701 0.77431 0.88788 0.94297 0.50799 0.00000 0.56779 0.59880 0.91871 1.08926 1.29393 1.25822 1.31980 1.23722 1.28288 1.21790 1.27393 1.39218 1.35777 1.38107 1.37415 1.24689 1.45273 1.35292 1.38124 1.33341 1.37884 1.36578 1.39380 1.50462 1.53421 1.83242 0.89949 0.99618 2.31905 Desulfuroc 0.79838 0.83616 0.65147 0.90042 0.94264 0.57542 0.56779 0.00000 0.03771 0.94432 0.88369 1.44824 1.41111 1.45758 1.26040 1.34867 1.24232 1.43768 1.48496 1.44569 1.47654 1.45640 1.36630 1.50552 1.45283 1.44043 1.43723 1.42285 1.40544 1.31486 1.49890 1.65734 1.83227 0.86346 0.96790 1.99858 Thermococ 0.80427 0.83612 0.64710 0.89933 0.94396 0.58274 0.59880 0.03771 0.00000 0.94946 0.88075 1.43528 1.40070 1.44092 1.26663 1.35183 1.26821 1.44084 1.48644 1.44719 1.47803 1.45203 1.40193 1.52711 1.47631 1.45231 1.44122 1.41838 1.41123 1.36135 1.52096 1.68117 1.85524 0.87054 0.98671 2.05320 Enterococ 1.13945 1.10096 1.04169 1.12885 1.13370 0.92882 0.91871 0.94432 0.94946 0.00000 1.26043 1.65646 1.65940 1.69126 1.49652 1.55372 1.38961 1.53114 1.54283 1.51467 1.56076 1.49811 1.46166 1.58174 1.54206 1.63093 1.59292 1.58159 1.56543 1.59249 1.75055 1.70927 2.33379 1.25831 1.43873 2.41376 Sulfolobus 1.32094 1.34417 1.07460 1.38360 1.39023 1.08937 1.08926 0.88369 0.88075 1.26043 0.00000 1.67896 1.71217 1.68903 1.66056 1.73029 1.57421 1.69678 1.77458 1.73236 1.77157 1.71604 1.63841 1.82481 1.69368 1.82070 1.67647 1.59102 1.59417 1.56485 1.84778 1.95196 2.27018 1.28092 1.42470 2.42561 Daucus 1.45077 1.44349 1.47308 1.57455 1.61288 1.41412 1.29393 1.44824 1.43528 1.65646 1.67896 0.00000 0.04623 0.06466 0.38407 0.37658 0.47671 0.66870 0.59007 0.58377 0.58533 0.57544 0.56282 0.67398 0.64578 0.65892 0.70837 0.85339 0.90683 0.80949 0.81810 0.84702 1.32018 1.30830 1.37704 2.89184 Gossypium 1.41267 1.40969 1.43681 1.57503 1.63247 1.41286 1.25822 1.41111 1.40070 1.65940 1.71217 0.04623 0.00000 0.07040 0.36727 0.38553 0.47301 0.63794 0.57057 0.56066 0.57015 0.55265 0.55326 0.66484 0.63976 0.64675 0.72785 0.83884 0.89286 0.80303 0.81173 0.82427 1.30716 1.33125 1.38566 2.78179 Arabidopsi 1.48362 1.48131 1.50349 1.63191 1.65958 1.43417 1.31980 1.45758 1.44092 1.69126 1.68903 0.06466 0.07040 0.00000 0.36851 0.36630 0.47659 0.65070 0.58719 0.57452 0.58335 0.56706 0.55267 0.67970 0.63580 0.65373 0.72716 0.84509 0.88677 0.82651 0.81634 0.84585 1.34170 1.34119 1.36880 2.84419 '1Acetab' 1.46987 1.45741 1.40977 1.49153 1.46540 1.36217 1.23722 1.26040 1.26663 1.49652 1.66056 0.38407 0.36727 0.36851 0.00000 0.05137 0.47259 0.62146 0.56930 0.56307 0.56479 0.57632 0.53384 0.63206 0.60528 0.62538 0.66904 0.76569 0.79087 0.77104 0.71244 0.78796 1.29381 1.33988 1.42310 2.68814 '2Acetab' 1.55851 1.53448 1.44718 1.53083 1.51995 1.41766 1.28288 1.34867 1.35183 1.55372 1.73029 0.37658 0.38553 0.36630 0.05137 0.00000 0.49703 0.66986 0.61254 0.61022 0.61392 0.61643 0.55953 0.67705 0.62495 0.66764 0.71215 0.78627 0.80989 0.80748 0.75016 0.83427 1.36778 1.41014 1.45756 2.78131 Cyanidium 1.27098 1.32609 1.36328 1.39957 1.42304 1.22359 1.21790 1.24232 1.26821 1.38961 1.57421 0.47671 0.47301 0.47659 0.47259 0.49703 0.00000 0.65500 0.50281 0.47613 0.47965 0.49608 0.54050 0.61868 0.59895 0.57203 0.64683 0.75745 0.74948 0.71682 0.72540 0.81862 1.24422 1.27405 1.31514 2.56290 Trypanos 1.43792 1.50226 1.58365 1.60295 1.60960 1.42966 1.27393 1.43768 1.44084 1.53114 1.69678 0.66870 0.63794 0.65070 0.62146 0.66986 0.65500 0.00000 0.73662 0.72081 0.75312 0.71607 0.75276 0.84312 0.77844 0.70174 0.75938 0.94383 0.91138 0.89011 0.81928 0.88516 1.46544 1.33623 1.41675 2.63394 Homo 1.54721 1.56970 1.63538 1.48524 1.57161 1.44906 1.39218 1.48496 1.48644 1.54283 1.77458 0.59007 0.57057 0.58719 0.56930 0.61254 0.50281 0.73662 0.00000 0.01989 0.03388 0.05761 0.23338 0.26874 0.26793 0.57696 0.67903 0.66666 0.68059 0.72956 0.61988 0.93342 1.45203 1.43764 1.46150 2.90075 Bos 1.49961 1.51923 1.57768 1.46530 1.54769 1.41678 1.35777 1.44569 1.44719 1.51467 1.73236 0.58377 0.56066 0.57452 0.56307 0.61022 0.47613 0.72081 0.01989 0.00000 0.01995 0.04290 0.22026 0.25387 0.25321 0.56135 0.66607 0.66907 0.66855 0.72657 0.60773 0.90749 1.43121 1.39619 1.42696 2.82911 Mus 1.54201 1.54718 1.60460 1.49029 1.56574 1.42237 1.38107 1.47654 1.47803 1.56076 1.77157 0.58533 0.57015 0.58335 0.56479 0.61392 0.47965 0.75312 0.03388 0.01995 0.00000 0.05755 0.22769 0.26599 0.26514 0.56569 0.68450 0.67375 0.68534 0.73787 0.62137 0.90452 1.45970 1.42881 1.46752 2.88528 Gallus 1.52137 1.54058 1.58438 1.49392 1.55291 1.43233 1.37415 1.45640 1.45203 1.49811 1.71604 0.57544 0.55265 0.56706 0.57632 0.61643 0.49608 0.71607 0.05761 0.04290 0.05755 0.00000 0.24451 0.27974 0.26647 0.55006 0.68897 0.68183 0.67990 0.73546 0.61670 0.89737 1.41375 1.36536 1.41585 2.80596 Manduca 1.45151 1.45602 1.45435 1.55686 1.52229 1.34313 1.24689 1.36630 1.40193 1.46166 1.63841 0.56282 0.55326 0.55267 0.53384 0.55953 0.54050 0.75276 0.23338 0.22026 0.22769 0.24451 0.00000 0.15342 0.16792 0.55008 0.65092 0.63828 0.63469 0.68898 0.64656 0.85973 1.33156 1.41610 1.42026 2.86177 Aedes 1.65462 1.69226 1.63879 1.74873 1.73916 1.56181 1.45273 1.50552 1.52711 1.58174 1.82481 0.67398 0.66484 0.67970 0.63206 0.67705 0.61868 0.84312 0.26874 0.25387 0.26599 0.27974 0.15342 0.00000 0.18817 0.65016 0.70326 0.71631 0.73076 0.80882 0.73077 0.95020 1.46714 1.57390 1.53807 3.20298 Drosophila 1.55585 1.58784 1.54195 1.63964 1.67852 1.45083 1.35292 1.45283 1.47631 1.54206 1.69368 0.64578 0.63976 0.63580 0.60528 0.62495 0.59895 0.77844 0.26793 0.25321 0.26514 0.26647 0.16792 0.18817 0.00000 0.58641 0.65143 0.72372 0.71388 0.75157 0.69294 0.92805 1.42969 1.49511 1.51428 3.07656 Dictyost 1.47664 1.53923 1.52754 1.62264 1.70049 1.43028 1.38124 1.44043 1.45231 1.63093 1.82070 0.65892 0.64675 0.65373 0.62538 0.66764 0.57203 0.70174 0.57696 0.56135 0.56569 0.55006 0.55008 0.65016 0.58641 0.00000 0.65973 0.74413 0.81079 0.81462 0.73391 0.86987 1.42438 1.37458 1.41494 2.79466 Entamoeba 1.32630 1.39396 1.39703 1.43029 1.41850 1.37383 1.33341 1.43723 1.44122 1.59292 1.67647 0.70837 0.72785 0.72716 0.66904 0.71215 0.64683 0.75938 0.67903 0.66607 0.68450 0.68897 0.65092 0.70326 0.65143 0.65973 0.00000 0.82426 0.80031 0.83749 0.76218 0.89139 1.40246 1.27777 1.37835 2.83202 Saccharom 1.56052 1.60536 1.48176 1.73008 1.65057 1.42445 1.37884 1.42285 1.41838 1.58159 1.59102 0.85339 0.83884 0.84509 0.76569 0.78627 0.75745 0.94383 0.66666 0.66907 0.67375 0.68183 0.63828 0.71631 0.72372 0.74413 0.82426 0.00000 0.15017 0.43479 0.52529 1.09775 1.47243 1.30595 1.26199 2.79917 Candida 1.49106 1.54127 1.48169 1.71820 1.65217 1.39188 1.36578 1.40544 1.41123 1.56543 1.59417 0.90683 0.89286 0.88677 0.79087 0.80989 0.74948 0.91138 0.68059 0.66855 0.68534 0.67990 0.63469 0.73076 0.71388 0.81079 0.80031 0.15017 0.00000 0.42701 0.49611 1.05167 1.47200 1.31988 1.29489 2.69027 Neurosp 1.50062 1.56201 1.54017 1.59548 1.50563 1.34593 1.39380 1.31486 1.36135 1.59249 1.56485 0.80949 0.80303 0.82651 0.77104 0.80748 0.71682 0.89011 0.72956 0.72657 0.73787 0.73546 0.68898 0.80882 0.75157 0.81462 0.83749 0.43479 0.42701 0.00000 0.60038 1.06699 1.50473 1.25082 1.28786 2.58200 Schizosac 1.61274 1.64585 1.65209 1.71581 1.62345 1.57470 1.50462 1.49890 1.52096 1.75055 1.84778 0.81810 0.81173 0.81634 0.71244 0.75016 0.72540 0.81928 0.61988 0.60773 0.62137 0.61670 0.64656 0.73077 0.69294 0.73391 0.76218 0.52529 0.49611 0.60038 0.00000 1.03730 1.47421 1.35797 1.36934 3.04643 Plasmodium 1.68136 1.68095 1.61336 1.86248 1.85222 1.68472 1.53421 1.65734 1.68117 1.70927 1.95196 0.84702 0.82427 0.84585 0.78796 0.83427 0.81862 0.88516 0.93342 0.90749 0.90452 0.89737 0.85973 0.95020 0.92805 0.86987 0.89139 1.09775 1.05167 1.06699 1.03730 0.00000 1.45534 1.42618 1.48170 2.80811 Giardia 2.09975 2.05864 2.01894 2.27823 2.18002 1.97596 1.83242 1.83227 1.85524 2.33379 2.27018 1.32018 1.30716 1.34170 1.29381 1.36778 1.24422 1.46544 1.45203 1.43121 1.45970 1.41375 1.33156 1.46714 1.42969 1.42438 1.40246 1.47243 1.47200 1.50473 1.47421 1.45534 0.00000 1.71427 1.73494 3.84056 Thermus 0.96853 1.02372 0.94229 1.03173 1.13912 0.89752 0.89949 0.86346 0.87054 1.25831 1.28092 1.30830 1.33125 1.34119 1.33988 1.41014 1.27405 1.33623 1.43764 1.39619 1.42881 1.36536 1.41610 1.57390 1.49511 1.37458 1.27777 1.30595 1.31988 1.25082 1.35797 1.42618 1.71427 0.00000 0.39932 2.78472 Deinococ 1.10582 1.17355 1.09850 1.18896 1.25195 1.08375 0.99618 0.96790 0.98671 1.43873 1.42470 1.37704 1.38566 1.36880 1.42310 1.45756 1.31514 1.41675 1.46150 1.42696 1.46752 1.41585 1.42026 1.53807 1.51428 1.41494 1.37835 1.26199 1.29489 1.28786 1.36934 1.48170 1.73494 0.39932 0.00000 2.55262 Borrelia 2.38562 2.58526 2.46322 2.38620 2.54292 2.31125 2.31905 1.99858 2.05320 2.41376 2.42561 2.89184 2.78179 2.84419 2.68814 2.78131 2.56290 2.63394 2.90075 2.82911 2.88528 2.80596 2.86177 3.20298 3.07656 2.79466 2.83202 2.79917 2.69027 2.58200 3.04643 2.80811 3.84056 2.78472 2.55262 0.00000 Average distance (over all possible pairs of sequences): 1.20704 TREE SEARCH 5 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. :----2 MMethanos : :---3 Archaeogl : :-------10 Enterococ : :--------11 Sulfolobus : :------------------36 Borrelia : : :-4 Haloferax :-----37 : :--5 Halobact : : :-8 Desulfuroc :---38 : :-9 Thermococ : : :--6 jMethanoco :--39 : :---7 Methanobac : : :--34 Thermus : :---40 : : :--35 Deinococ :--52 : : :---------33 Giardia : : : : :----18 Trypanos : : : :-----32 Plasmodium : : : :----27 Entamoeba : : : :---26 Dictyost : ------51 : :---17 Cyanidium : : : : :---31 Schizosac : :---42 : : :---30 Neurosp : : : : : : :-28 Saccharom : : :--41 : : :-29 Candida : : : : :-22 Gallus : :--45 : : : :-21 Mus : : :-44 : : : :-19 Homo : : :-43 : : :-20 Bos : : : : :-15 '1Acetab' : :---46 : : :-16 '2Acetab' : : : : :-14 Arabidopsi : :---48 : : : :-12 Daucus : : :-47 : : :-13 Gossypium : : : : :-23 Manduca : :--50 : : :-24 Aedes : :-49 : :-25 Drosophila : :---1 BMethanos branch length S.E. branch length S.E. BMethanos 1 0.39852 0.04386 37 0.61554 0.06163 MMethanos 2 0.44846 0.04704 38 0.42865 0.04588 Archaeogl 3 0.42714 0.04567 39 0.22412 0.03608 Haloferax 4 0.11326 0.02365 40 0.36584 0.05344 Halobact 5 0.15821 0.02575 41 0.17790 0.02726 jMethanoco 6 0.27169 0.03672 42 0.36946 0.04141 Methanobac 7 0.32009 0.03958 43 0.00190 0.00193 Desulfuroc 8 0.02015 0.00843 44 0.01228 0.00668 Thermococ 9 0.02390 0.00875 45 0.23571 0.02889 Enterococ 10 0.87335 0.07654 46 0.37626 0.03757 Sulfolobus 11 1.02778 0.08763 47 0.01566 0.00809 Daucus 12 0.02350 0.00712 48 0.36797 0.03706 Gossypium 13 0.02713 0.00761 49 0.01659 0.00860 Arabidopsi 14 0.03650 0.00981 50 0.22405 0.02853 '1Acetab' 15 0.00488 0.00482 51 0.80275 0.08089 '2Acetab' 16 0.05122 0.01038 52 0.27382 0.04892 Cyanidium 17 0.39117 0.04050 Trypanos 18 0.56505 0.05039 Homo 19 0.01981 0.00615 Bos 20 0.00220 0.00228 Mus 21 0.01794 0.00584 Gallus 22 0.03167 0.00869 Manduca 23 0.06177 0.01306 Aedes 24 0.09687 0.01572 Drosophila 25 0.10965 0.01662 Dictyost 26 0.42672 0.04073 Entamoeba 27 0.52297 0.04767 Saccharom 28 0.08423 0.01570 Candida 29 0.07323 0.01506 Neurosp 30 0.32631 0.03645 Schizosac 31 0.30202 0.03483 Plasmodium 32 0.70059 0.05969 Giardia 33 1.25508 0.10090 Thermus 34 0.17817 0.03220 Deinococ 35 0.28226 0.03741 35 iterations until convergence Borrelia 36 2.48670 0.23441 log L: -22631.11 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.39852,MMethanos:0.44846,Archaeogl:0.42714,Enterococ:0.87335, Sulfolobus:1.02778,Borrelia:2.48670,(Haloferax:0.11326,Halobact:0.15821) :0.61554,(Desulfuroc:0.02015,Thermococ:0.02390):0.42865,(jMethanoco:0.27169, Methanobac:0.32009):0.22412,((Thermus:0.17817,Deinococ:0.28226) :0.36584,(Giardia:1.25508,Trypanos:0.56505,Plasmodium:0.70059,Entamoeba:0.52297, Dictyost:0.42672,Cyanidium:0.39117,(Schizosac:0.30202,Neurosp:0.32631, (Saccharom:0.08423,Candida:0.07323):0.17790):0.36946,(Gallus:0.03167, (Mus:0.01794,(Homo:0.01981,Bos:0.00220):0.00190):0.01228):0.23571, ('1Acetab':0.00488,'2Acetab':0.05122):0.37626,(Arabidopsi:0.03650, (Daucus:0.02350,Gossypium:0.02713):0.01566):0.36797,(Manduca:0.06177, (Aedes:0.09687,Drosophila:0.10965):0.01659):0.22405):0.80275):0.27382); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :----2 MMethanos : :---3 Archaeogl : :-------10 Enterococ : :--------11 Sulfolobus : :------------------36 Borrelia : : :-4 Haloferax :-----37 : :--5 Halobact : : :-8 Desulfuroc :---38 : :-9 Thermococ : : :--6 jMethanoco :--39 : :---7 Methanobac : : :--34 Thermus : :---40 : : :--35 Deinococ :--53 : : :--------33 Giardia : :-----52 : : :----18 Trypanos : : : : :-----32 Plasmodium : : : :----27 Entamoeba : : : :---26 Dictyost : : : :---17 Cyanidium : --51 : : :---31 Schizosac : :---42 : : :---30 Neurosp : : : : : : :-28 Saccharom : : :--41 : : :-29 Candida : : : : :-22 Gallus : :--45 : : : :-21 Mus : : :-44 : : : :-19 Homo : : :-43 : : :-20 Bos : : : : :-15 '1Acetab' : :---46 : : :-16 '2Acetab' : : : : :-14 Arabidopsi : :---48 : : : :-12 Daucus : : :-47 : : :-13 Gossypium : : : : :-23 Manduca : :--50 : : :-24 Aedes : :-49 : :-25 Drosophila : :---1 BMethanos branch length S.E. branch length S.E. BMethanos 1 0.39874 0.04392 37 0.61697 0.06175 MMethanos 2 0.44748 0.04699 38 0.42886 0.04592 Archaeogl 3 0.42662 0.04569 39 0.22494 0.03618 Haloferax 4 0.11307 0.02363 40 0.36083 0.05320 Halobact 5 0.15802 0.02572 41 0.17742 0.02721 jMethanoco 6 0.26945 0.03658 42 0.36949 0.04142 Methanobac 7 0.32136 0.03965 43 0.00190 0.00193 Desulfuroc 8 0.02022 0.00843 44 0.01231 0.00669 Thermococ 9 0.02374 0.00873 45 0.23486 0.02882 Enterococ 10 0.86943 0.07624 46 0.37560 0.03753 Sulfolobus 11 1.02866 0.08775 47 0.01571 0.00810 Daucus 12 0.02351 0.00712 48 0.36698 0.03699 Gossypium 13 0.02707 0.00760 49 0.01664 0.00860 Arabidopsi 14 0.03640 0.00980 50 0.22310 0.02845 '1Acetab' 15 0.00481 0.00480 51 0.21416 0.05247 '2Acetab' 16 0.05124 0.01037 52 0.59844 0.07484 Cyanidium 17 0.39078 0.04045 53 0.27441 0.04882 Trypanos 18 0.56300 0.05023 Homo 19 0.01978 0.00614 Bos 20 0.00220 0.00228 Mus 21 0.01792 0.00583 Gallus 22 0.03158 0.00867 Manduca 23 0.06158 0.01303 Aedes 24 0.09670 0.01569 Drosophila 25 0.10953 0.01660 Dictyost 26 0.42599 0.04066 Entamoeba 27 0.52167 0.04757 Saccharom 28 0.08393 0.01567 Candida 29 0.07328 0.01506 Neurosp 30 0.32561 0.03639 Schizosac 31 0.30182 0.03479 Plasmodium 32 0.69819 0.05951 Giardia 33 1.02378 0.09468 Thermus 34 0.17501 0.03190 Deinococ 35 0.28515 0.03747 39 iterations until convergence Borrelia 36 2.48431 0.23432 log L: -22619.41 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.39874,MMethanos:0.44748,Archaeogl:0.42662,Enterococ:0.86943, Sulfolobus:1.02866,Borrelia:2.48431,(Haloferax:0.11307,Halobact:0.15802) :0.61697,(Desulfuroc:0.02022,Thermococ:0.02374):0.42886,(jMethanoco:0.26945, Methanobac:0.32136):0.22494,((Thermus:0.17501,Deinococ:0.28515) :0.36083,(Giardia:1.02378,(Trypanos:0.56300,Plasmodium:0.69819,Entamoeba:0.52167, Dictyost:0.42599,Cyanidium:0.39078,(Schizosac:0.30182,Neurosp:0.32561, (Saccharom:0.08393,Candida:0.07328):0.17742):0.36949,(Gallus:0.03158, (Mus:0.01792,(Homo:0.01978,Bos:0.00220):0.00190):0.01231):0.23486, ('1Acetab':0.00481,'2Acetab':0.05124):0.37560,(Arabidopsi:0.03640, (Daucus:0.02351,Gossypium:0.02707):0.01571):0.36698,(Manduca:0.06158, (Aedes:0.09670,Drosophila:0.10953):0.01664):0.22310):0.21416):0.59844) :0.27441); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :----2 MMethanos : :---3 Archaeogl : :------10 Enterococ : :--------11 Sulfolobus : :------------------36 Borrelia : : :-4 Haloferax :-----37 : :--5 Halobact : : :-8 Desulfuroc :---38 : :-9 Thermococ : : :--6 jMethanoco :--39 : :---7 Methanobac : : :--34 Thermus : :---40 : : :--35 Deinococ :--54 : : :-------33 Giardia : :----53 : : :----18 Trypanos : :--52 : : :-----32 Plasmodium : : : : :----27 Entamoeba : : : :---26 Dictyost : : : :---17 Cyanidium : -51 : : :---31 Schizosac : :---42 : : :---30 Neurosp : : : : : : :-28 Saccharom : : :--41 : : :-29 Candida : : : : :-22 Gallus : :--45 : : : :-21 Mus : : :-44 : : : :-19 Homo : : :-43 : : :-20 Bos : : : : :-15 '1Acetab' : :---46 : : :-16 '2Acetab' : : : : :-14 Arabidopsi : :---48 : : : :-12 Daucus : : :-47 : : :-13 Gossypium : : : : :-23 Manduca : :--50 : : :-24 Aedes : :-49 : :-25 Drosophila : :---1 BMethanos branch length S.E. branch length S.E. BMethanos 1 0.39911 0.04382 37 0.61469 0.06143 MMethanos 2 0.44880 0.04694 38 0.42631 0.04563 Archaeogl 3 0.42618 0.04557 39 0.22187 0.03582 Haloferax 4 0.11270 0.02358 40 0.35713 0.05247 Halobact 5 0.15791 0.02568 41 0.17642 0.02707 jMethanoco 6 0.26888 0.03642 42 0.36822 0.04129 Methanobac 7 0.32032 0.03948 43 0.00189 0.00193 Desulfuroc 8 0.02061 0.00845 44 0.01229 0.00666 Thermococ 9 0.02325 0.00867 45 0.23118 0.02853 Enterococ 10 0.86233 0.07550 46 0.37503 0.03743 Sulfolobus 11 1.02316 0.08720 47 0.01577 0.00809 Daucus 12 0.02352 0.00711 48 0.36618 0.03690 Gossypium 13 0.02694 0.00758 49 0.01669 0.00860 Arabidopsi 14 0.03619 0.00977 50 0.21957 0.02814 '1Acetab' 15 0.00477 0.00481 51 0.10619 0.03224 '2Acetab' 16 0.05115 0.01035 52 0.15071 0.04717 Cyanidium 17 0.38933 0.04026 53 0.56197 0.07247 Trypanos 18 0.45771 0.04800 54 0.27210 0.04806 Homo 19 0.01972 0.00612 Bos 20 0.00220 0.00228 Mus 21 0.01787 0.00582 Gallus 22 0.03148 0.00864 Manduca 23 0.06136 0.01300 Aedes 24 0.09650 0.01566 Drosophila 25 0.10920 0.01655 Dictyost 26 0.42466 0.04050 Entamoeba 27 0.51775 0.04728 Saccharom 28 0.08333 0.01561 Candida 29 0.07348 0.01505 Neurosp 30 0.32491 0.03627 Schizosac 31 0.30112 0.03469 Plasmodium 32 0.69868 0.05949 Giardia 33 1.00772 0.09388 Thermus 34 0.17772 0.03187 Deinococ 35 0.28115 0.03714 42 iterations until convergence Borrelia 36 2.45895 0.23119 log L: -22611.78 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.39911,MMethanos:0.44880,Archaeogl:0.42618,Enterococ:0.86233, Sulfolobus:1.02316,Borrelia:2.45895,(Haloferax:0.11270,Halobact:0.15791) :0.61469,(Desulfuroc:0.02061,Thermococ:0.02325):0.42631,(jMethanoco:0.26888, Methanobac:0.32032):0.22187,((Thermus:0.17772,Deinococ:0.28115) :0.35713,(Giardia:1.00772,(Trypanos:0.45771,(Plasmodium:0.69868, Entamoeba:0.51775,Dictyost:0.42466,Cyanidium:0.38933,(Schizosac:0.30112, Neurosp:0.32491,(Saccharom:0.08333,Candida:0.07348):0.17642):0.36822, (Gallus:0.03148,(Mus:0.01787,(Homo:0.01972,Bos:0.00220):0.00189):0.01229) :0.23118,('1Acetab':0.00477,'2Acetab':0.05115):0.37503,(Arabidopsi:0.03619, (Daucus:0.02352,Gossypium:0.02694):0.01577):0.36618,(Manduca:0.06136, (Aedes:0.09650,Drosophila:0.10920):0.01669):0.21957):0.10619):0.15071) :0.56197):0.27210); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :----2 MMethanos : :---3 Archaeogl : :------10 Enterococ : :--------11 Sulfolobus : :-----------------36 Borrelia : : :-4 Haloferax :-----37 : :--5 Halobact : : :-8 Desulfuroc :---38 : :-9 Thermococ : : :--6 jMethanoco :--39 : :---7 Methanobac : : :--34 Thermus : :---40 : : :--35 Deinococ :--55 : : :-------33 Giardia : :----54 : : :----18 Trypanos : :--53 : : :-----32 Plasmodium : : : : :----27 Entamoeba : : : :---26 Dictyost : : : :---17 Cyanidium : -52 : : :-15 '1Acetab' : : :--41 : : : :-16 '2Acetab' : :--44 : : : :-14 Arabidopsi : : :--43 : : : :-12 Daucus : : :-42 : : :-13 Gossypium : : : : :---31 Schizosac : :---46 : : :---30 Neurosp : : : : : : :-28 Saccharom : : :--45 : : :-29 Candida : : : : :-22 Gallus : :--49 : : : :-21 Mus : : :-48 : : : :-19 Homo : : :-47 : : :-20 Bos : : : : :-23 Manduca : :--51 : : :-24 Aedes : :-50 : :-25 Drosophila : :---1 BMethanos branch length S.E. branch length S.E. BMethanos 1 0.39078 0.04306 37 0.60399 0.06052 MMethanos 2 0.44395 0.04641 38 0.42378 0.04527 Archaeogl 3 0.41860 0.04483 39 0.21714 0.03524 Haloferax 4 0.11270 0.02332 40 0.35776 0.05238 Halobact 5 0.15447 0.02528 41 0.19537 0.02746 jMethanoco 6 0.26565 0.03597 42 0.02602 0.00887 Methanobac 7 0.31611 0.03896 43 0.18754 0.02713 Desulfuroc 8 0.02008 0.00832 44 0.23238 0.03083 Thermococ 9 0.02315 0.00857 45 0.17051 0.02650 Enterococ 10 0.84798 0.07438 46 0.35896 0.04043 Sulfolobus 11 1.01587 0.08661 47 0.00187 0.00190 Daucus 12 0.02330 0.00703 48 0.01202 0.00640 Gossypium 13 0.02639 0.00744 49 0.19407 0.02572 Arabidopsi 14 0.02542 0.00892 50 0.01554 0.00812 '1Acetab' 15 0.00947 0.00622 51 0.18305 0.02515 '2Acetab' 16 0.04580 0.00999 52 0.11409 0.03346 Cyanidium 17 0.39623 0.04044 53 0.15229 0.04708 Trypanos 18 0.45436 0.04787 54 0.56128 0.07241 Homo 19 0.01946 0.00604 55 0.26820 0.04782 Bos 20 0.00219 0.00225 Mus 21 0.01765 0.00574 Gallus 22 0.03117 0.00849 Manduca 23 0.06200 0.01290 Aedes 24 0.09615 0.01553 Drosophila 25 0.10764 0.01635 Dictyost 26 0.41732 0.03971 Entamoeba 27 0.51077 0.04666 Saccharom 28 0.08232 0.01541 Candida 29 0.07247 0.01485 Neurosp 30 0.32341 0.03603 Schizosac 31 0.30101 0.03457 Plasmodium 32 0.70979 0.05984 Giardia 33 0.98250 0.09212 Thermus 34 0.17543 0.03162 Deinococ 35 0.27781 0.03676 32 iterations until convergence Borrelia 36 2.42197 0.22770 log L: -22523.31 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.39078,MMethanos:0.44395,Archaeogl:0.41860,Enterococ:0.84798, Sulfolobus:1.01587,Borrelia:2.42197,(Haloferax:0.11270,Halobact:0.15447) :0.60399,(Desulfuroc:0.02008,Thermococ:0.02315):0.42378,(jMethanoco:0.26565, Methanobac:0.31611):0.21714,((Thermus:0.17543,Deinococ:0.27781) :0.35776,(Giardia:0.98250,(Trypanos:0.45436,(Plasmodium:0.70979, Entamoeba:0.51077,Dictyost:0.41732,Cyanidium:0.39623,(('1Acetab':0.00947, '2Acetab':0.04580):0.19537,(Arabidopsi:0.02542,(Daucus:0.02330, Gossypium:0.02639):0.02602):0.18754):0.23238,(Schizosac:0.30101, Neurosp:0.32341,(Saccharom:0.08232,Candida:0.07247):0.17051):0.35896, (Gallus:0.03117,(Mus:0.01765,(Homo:0.01946,Bos:0.00219):0.00187):0.01202) :0.19407,(Manduca:0.06200,(Aedes:0.09615,Drosophila:0.10764):0.01554) :0.18305):0.11409):0.15229):0.56128):0.26820); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 5 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :----2 MMethanos : :---3 Archaeogl : :------10 Enterococ : :--------11 Sulfolobus : :-----------------36 Borrelia : : :-4 Haloferax :-----37 : :--5 Halobact : : :-8 Desulfuroc :---38 : :-9 Thermococ : : :--6 jMethanoco :--39 : :---7 Methanobac : : :--34 Thermus : :---40 : : :--35 Deinococ :--56 : : :-------33 Giardia : :----55 : : :----18 Trypanos : :--54 : : :-----32 Plasmodium : : : : :----27 Entamoeba : : : :---26 Dictyost : -53 : : :--17 Cyanidium : :--45 : : : :-15 '1Acetab' : : : :--41 : : : : :-16 '2Acetab' : : :-44 : : : :-14 Arabidopsi : : :--43 : : : :-12 Daucus : : :-42 : : :-13 Gossypium : : : : :---31 Schizosac : :---47 : : :---30 Neurosp : : : : : : :-28 Saccharom : : :--46 : : :-29 Candida : : : : :-22 Gallus : :--50 : : : :-21 Mus : : :-49 : : : :-19 Homo : : :-48 : : :-20 Bos : : : : :-23 Manduca : :--52 : : :-24 Aedes : :-51 : :-25 Drosophila : :---1 BMethanos branch length S.E. branch length S.E. BMethanos 1 0.38818 0.04275 37 0.60069 0.06011 MMethanos 2 0.44137 0.04612 38 0.42180 0.04502 Archaeogl 3 0.41580 0.04450 39 0.21543 0.03499 Haloferax 4 0.11248 0.02323 40 0.35463 0.05202 Halobact 5 0.15339 0.02513 41 0.19776 0.02739 jMethanoco 6 0.26424 0.03575 42 0.02579 0.00889 Methanobac 7 0.31441 0.03874 43 0.17638 0.02626 Desulfuroc 8 0.01991 0.00826 44 0.12163 0.02488 Thermococ 9 0.02304 0.00853 45 0.15568 0.02741 Enterococ 10 0.84188 0.07381 46 0.16595 0.02609 Sulfolobus 11 1.00865 0.08597 47 0.35260 0.03972 Daucus 12 0.02294 0.00696 48 0.00186 0.00189 Gossypium 13 0.02673 0.00745 49 0.01158 0.00636 Arabidopsi 14 0.02537 0.00890 50 0.18079 0.02457 '1Acetab' 15 0.01320 0.00681 51 0.01452 0.00769 '2Acetab' 16 0.04183 0.00970 52 0.16607 0.02386 Cyanidium 17 0.27221 0.03408 53 0.11568 0.03349 Trypanos 18 0.45732 0.04808 54 0.15133 0.04679 Homo 19 0.01935 0.00601 55 0.55506 0.07169 Bos 20 0.00218 0.00225 56 0.26863 0.04772 Mus 21 0.01755 0.00571 Gallus 22 0.03135 0.00848 Manduca 23 0.06245 0.01280 Aedes 24 0.09588 0.01546 Drosophila 25 0.10717 0.01625 Dictyost 26 0.41654 0.03959 Entamoeba 27 0.50175 0.04599 Saccharom 28 0.08181 0.01529 Candida 29 0.07217 0.01475 Neurosp 30 0.32376 0.03594 Schizosac 31 0.30114 0.03445 Plasmodium 32 0.71104 0.05979 Giardia 33 0.97545 0.09142 Thermus 34 0.17319 0.03144 Deinococ 35 0.27734 0.03663 34 iterations until convergence Borrelia 36 2.40432 0.22578 log L: -22485.08 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.38818,MMethanos:0.44137,Archaeogl:0.41580,Enterococ:0.84188, Sulfolobus:1.00865,Borrelia:2.40432,(Haloferax:0.11248,Halobact:0.15339) :0.60069,(Desulfuroc:0.01991,Thermococ:0.02304):0.42180,(jMethanoco:0.26424, Methanobac:0.31441):0.21543,((Thermus:0.17319,Deinococ:0.27734) :0.35463,(Giardia:0.97545,(Trypanos:0.45732,(Plasmodium:0.71104, Entamoeba:0.50175,Dictyost:0.41654,(Cyanidium:0.27221,(('1Acetab':0.01320, '2Acetab':0.04183):0.19776,(Arabidopsi:0.02537,(Daucus:0.02294, Gossypium:0.02673):0.02579):0.17638):0.12163):0.15568,(Schizosac:0.30114, Neurosp:0.32376,(Saccharom:0.08181,Candida:0.07217):0.16595):0.35260, (Gallus:0.03135,(Mus:0.01755,(Homo:0.01935,Bos:0.00218):0.00186):0.01158) :0.18079,(Manduca:0.06245,(Aedes:0.09588,Drosophila:0.10717):0.01452) :0.16607):0.11568):0.15133):0.55506):0.26863); COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. Significantly worse -------------------------------------------------------- 1 -22631.11 146.03 24.15 yes 2 -22619.41 134.34 23.10 yes 3 -22611.78 126.70 22.44 yes 4 -22523.31 38.23 11.29 yes 5 -22485.08 0.00 <----------------- best tree This test (5% significance) follows Kishino and Hasegawa (1989). TIME STAMP Date and time: Tue May 28 23:28:32 2002 Runtime (excl. input) : 7934 seconds (= 132.2 minutes = 2.2 hours) Runtime (incl. input) : 8184 seconds (= 136.4 minutes = 2.3 hours)