TREE-PUZZLE 5.0 Input file name: infile User tree file name: intree Type of analysis: tree reconstruction Parameter estimation: accurate (slow) 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: uniform rate 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 0.14292 0.42914 0.50545 0.49415 0.55654 0.57699 0.53107 0.53156 0.70410 0.79297 0.81249 0.79924 0.82175 0.82786 0.86003 0.75257 0.80495 0.85912 0.83742 0.85517 0.84396 0.82078 0.88718 0.85764 0.81941 0.76633 0.85782 0.83784 0.83788 0.87998 0.90840 1.00964 0.60166 0.67490 1.12338 MMethanos 0.14292 0.00000 0.44909 0.51833 0.53453 0.58955 0.61148 0.56292 0.56200 0.69542 0.80074 0.81297 0.80044 0.82300 0.82300 0.85176 0.77226 0.82916 0.86764 0.84571 0.85634 0.85199 0.82197 0.90348 0.87177 0.84432 0.79597 0.87540 0.85891 0.86446 0.88854 0.90863 0.99885 0.63590 0.71387 1.18111 Archaeogl 0.42914 0.44909 0.00000 0.54265 0.58651 0.46988 0.52316 0.45644 0.45180 0.65274 0.67443 0.81413 0.79680 0.82318 0.80136 0.81680 0.77469 0.84920 0.88332 0.85855 0.86893 0.85672 0.81509 0.87465 0.84186 0.82613 0.77899 0.81859 0.81820 0.84558 0.88351 0.86703 0.98702 0.58902 0.66908 1.13905 Haloferax 0.50545 0.51833 0.54265 0.00000 0.20326 0.58152 0.58874 0.59193 0.59163 0.69779 0.81366 0.84667 0.84709 0.86601 0.83942 0.85389 0.80618 0.87401 0.82511 0.81583 0.82477 0.82959 0.85378 0.91476 0.87066 0.87237 0.80179 0.91756 0.91483 0.86301 0.90678 0.97890 1.07954 0.63953 0.72638 1.12826 Halobact 0.49415 0.53453 0.58651 0.20326 0.00000 0.61556 0.61906 0.61929 0.61758 0.70001 0.81868 0.87394 0.88188 0.89059 0.84210 0.86292 0.82076 0.88146 0.87521 0.86658 0.87284 0.87089 0.85238 0.92388 0.90007 0.91023 0.80279 0.90091 0.90736 0.84646 0.89075 0.97510 1.05121 0.69758 0.75993 1.18175 jMethanoco 0.55654 0.58955 0.46988 0.58152 0.61556 0.00000 0.37722 0.41106 0.41556 0.59042 0.68422 0.79025 0.78545 0.79254 0.77566 0.79818 0.71948 0.79994 0.81044 0.79779 0.79766 0.80365 0.77002 0.84574 0.80441 0.79132 0.77317 0.81074 0.80504 0.77286 0.86205 0.89793 0.97445 0.55841 0.66678 1.09976 Methanobac 0.57699 0.61148 0.52316 0.58874 0.61906 0.37722 0.00000 0.41507 0.43512 0.59455 0.69894 0.74443 0.72592 0.74959 0.72724 0.74772 0.72802 0.73726 0.78899 0.77343 0.78211 0.78296 0.73359 0.80389 0.77245 0.77619 0.75439 0.78744 0.78616 0.79971 0.84041 0.85154 0.93208 0.57636 0.63266 1.08603 Desulfuroc 0.53107 0.56292 0.45644 0.59193 0.61929 0.41106 0.41507 0.00000 0.03673 0.61396 0.60442 0.81029 0.79017 0.81100 0.74355 0.78003 0.73841 0.81760 0.83778 0.81890 0.83212 0.82673 0.79085 0.83875 0.82127 0.81305 0.80571 0.81307 0.80597 0.76948 0.84372 0.90794 0.92046 0.56151 0.61817 0.99773 Thermococ 0.53156 0.56200 0.45180 0.59163 0.61758 0.41556 0.43512 0.03673 0.00000 0.61790 0.60205 0.80274 0.78457 0.80188 0.74669 0.78102 0.74926 0.81948 0.83574 0.81684 0.83006 0.82225 0.80638 0.84836 0.82992 0.81673 0.80800 0.81062 0.80846 0.78977 0.84931 0.91523 0.92731 0.56141 0.62670 1.01885 Enterococ 0.70410 0.69542 0.65274 0.69779 0.70001 0.59042 0.59455 0.61396 0.61790 0.00000 0.76574 0.88763 0.88780 0.89718 0.83803 0.85678 0.79052 0.83659 0.84682 0.83581 0.85508 0.83347 0.81795 0.85757 0.84089 0.87784 0.86074 0.86565 0.86613 0.86847 0.93244 0.91789 1.10539 0.73870 0.82896 1.13918 Sulfolobus 0.79297 0.80074 0.67443 0.81366 0.81868 0.68422 0.69894 0.60442 0.60205 0.76574 0.00000 0.89278 0.90204 0.89769 0.90831 0.93250 0.87337 0.91489 0.93158 0.91687 0.93142 0.91029 0.89437 0.94959 0.90734 0.95407 0.88588 0.87754 0.88038 0.87432 0.97317 1.00427 1.09623 0.75630 0.84000 1.14451 Daucus 0.81249 0.81297 0.81413 0.84667 0.87394 0.79025 0.74443 0.81029 0.80274 0.88763 0.89278 0.00000 0.04470 0.06086 0.30266 0.29430 0.35285 0.45754 0.41903 0.41651 0.41672 0.41164 0.40807 0.45829 0.44671 0.47127 0.48303 0.55583 0.58309 0.53453 0.53799 0.55398 0.75997 0.75285 0.79662 1.26802 Gossypium 0.79924 0.80044 0.79680 0.84709 0.88188 0.78545 0.72592 0.79017 0.78457 0.88780 0.90204 0.04470 0.00000 0.06586 0.29265 0.30106 0.35137 0.43871 0.40558 0.40010 0.40577 0.39523 0.40108 0.45227 0.44327 0.46329 0.49651 0.54990 0.57652 0.53251 0.53521 0.53993 0.74874 0.75984 0.79772 1.23484 Arabidopsi 0.82175 0.82300 0.82318 0.86601 0.89059 0.79254 0.74959 0.81100 0.80188 0.89718 0.89769 0.06086 0.06586 0.00000 0.29285 0.28665 0.35049 0.44523 0.41552 0.40803 0.41399 0.40698 0.39848 0.45783 0.43979 0.46373 0.48932 0.55246 0.57416 0.54124 0.53667 0.55209 0.76955 0.76324 0.79261 1.24556 '1Acetab' 0.82786 0.82300 0.80136 0.83942 0.84210 0.77566 0.72724 0.74355 0.74669 0.83803 0.90831 0.30266 0.29265 0.29285 0.00000 0.04898 0.35415 0.42808 0.41127 0.40542 0.40549 0.41558 0.39186 0.43601 0.42684 0.44396 0.45953 0.51554 0.52597 0.51711 0.48798 0.52774 0.75978 0.77302 0.81680 1.21904 '2Acetab' 0.86003 0.85176 0.81680 0.85389 0.86292 0.79818 0.74772 0.78003 0.78102 0.85678 0.93250 0.29430 0.30106 0.28665 0.04898 0.00000 0.36453 0.45320 0.43529 0.43310 0.43452 0.43840 0.40608 0.46031 0.43815 0.46477 0.48316 0.52496 0.53459 0.53405 0.50747 0.55072 0.79064 0.80118 0.82700 1.24769 Cyanidium 0.75257 0.77226 0.77469 0.80618 0.82076 0.71948 0.72802 0.73841 0.74926 0.79052 0.87337 0.35285 0.35137 0.35049 0.35415 0.36453 0.00000 0.44893 0.36748 0.34948 0.35151 0.36527 0.39580 0.43157 0.42298 0.40656 0.44797 0.50984 0.50594 0.49054 0.49792 0.53326 0.73223 0.75080 0.78263 1.18616 Trypanos 0.80495 0.82916 0.84920 0.87401 0.88146 0.79994 0.73726 0.81760 0.81948 0.83659 0.91489 0.45754 0.43871 0.44523 0.42808 0.45320 0.44893 0.00000 0.48058 0.47200 0.48892 0.46918 0.49638 0.53183 0.50117 0.47267 0.49943 0.58474 0.57926 0.57662 0.53073 0.55690 0.80548 0.76244 0.80908 1.20639 Homo 0.85912 0.86764 0.88332 0.82511 0.87521 0.81044 0.78899 0.83778 0.83574 0.84682 0.93158 0.41903 0.40558 0.41552 0.41127 0.43529 0.36748 0.48058 0.00000 0.01970 0.03310 0.05525 0.20025 0.21925 0.22073 0.41394 0.46131 0.46260 0.47399 0.49842 0.44104 0.59522 0.81425 0.80686 0.82796 1.27939 Bos 0.83742 0.84571 0.85855 0.81583 0.86658 0.79779 0.77343 0.81890 0.81684 0.83581 0.91687 0.41651 0.40010 0.40803 0.40542 0.43310 0.34948 0.47200 0.01970 0.00000 0.01969 0.04151 0.18874 0.20733 0.20965 0.40297 0.45336 0.46444 0.46558 0.49593 0.43198 0.58133 0.80389 0.78674 0.81176 1.25834 Mus 0.85517 0.85634 0.86893 0.82477 0.87284 0.79766 0.78211 0.83212 0.83006 0.85508 0.93142 0.41672 0.40577 0.41399 0.40549 0.43452 0.35151 0.48892 0.03310 0.01969 0.00000 0.05520 0.19438 0.21585 0.21824 0.40706 0.46442 0.46764 0.47680 0.50246 0.44291 0.58310 0.81450 0.80084 0.83018 1.27329 Gallus 0.84396 0.85199 0.85672 0.82959 0.87089 0.80365 0.78296 0.82673 0.82225 0.83347 0.91029 0.41164 0.39523 0.40698 0.41558 0.43840 0.36527 0.46918 0.05525 0.04151 0.05520 0.00000 0.20706 0.22649 0.21948 0.39667 0.46689 0.47352 0.47474 0.50367 0.43906 0.57755 0.80015 0.77379 0.80951 1.24758 Manduca 0.82078 0.82197 0.81509 0.85378 0.85238 0.77002 0.73359 0.79085 0.80638 0.81795 0.89437 0.40807 0.40108 0.39848 0.39186 0.40608 0.39580 0.49638 0.20025 0.18874 0.19438 0.20706 0.00000 0.13441 0.14798 0.39983 0.44966 0.45534 0.45206 0.48648 0.45737 0.56408 0.76965 0.79702 0.81526 1.26523 Aedes 0.88718 0.90348 0.87465 0.91476 0.92388 0.84574 0.80389 0.83875 0.84836 0.85757 0.94959 0.45829 0.45227 0.45783 0.43601 0.46031 0.43157 0.53183 0.21925 0.20733 0.21585 0.22649 0.13441 0.00000 0.16045 0.44618 0.46908 0.48525 0.49404 0.53472 0.49236 0.59492 0.81238 0.85118 0.84557 1.33810 Drosophila 0.85764 0.87177 0.84186 0.87066 0.90007 0.80441 0.77245 0.82127 0.82992 0.84089 0.90734 0.44671 0.44327 0.43979 0.42684 0.43815 0.42298 0.50117 0.22073 0.20965 0.21824 0.21948 0.14798 0.16045 0.00000 0.41326 0.44926 0.50203 0.49532 0.51694 0.47790 0.58731 0.80289 0.82046 0.84892 1.30611 Dictyost 0.81941 0.84432 0.82613 0.87237 0.91023 0.79132 0.77619 0.81305 0.81673 0.87784 0.95407 0.47127 0.46329 0.46373 0.44396 0.46477 0.40656 0.47267 0.41394 0.40297 0.40706 0.39667 0.39983 0.44618 0.41326 0.00000 0.45422 0.49972 0.54349 0.54724 0.49884 0.55886 0.79901 0.75864 0.80014 1.24445 Entamoeba 0.76633 0.79597 0.77899 0.80179 0.80279 0.77317 0.75439 0.80571 0.80800 0.86074 0.88588 0.48303 0.49651 0.48932 0.45953 0.48316 0.44797 0.49943 0.46131 0.45336 0.46442 0.46689 0.44966 0.46908 0.44926 0.45422 0.00000 0.53781 0.52489 0.54822 0.50690 0.57208 0.78654 0.72814 0.78839 1.25526 Saccharom 0.85782 0.87540 0.81859 0.91756 0.90091 0.81074 0.78744 0.81307 0.81062 0.86565 0.87754 0.55583 0.54990 0.55246 0.51554 0.52496 0.50984 0.58474 0.46260 0.46444 0.46764 0.47352 0.45534 0.48525 0.50203 0.49972 0.53781 0.00000 0.13357 0.32481 0.38180 0.66631 0.80997 0.76117 0.74334 1.23895 Candida 0.83784 0.85891 0.81820 0.91483 0.90736 0.80504 0.78616 0.80597 0.80846 0.86613 0.88038 0.58309 0.57652 0.57416 0.52597 0.53459 0.50594 0.57926 0.47399 0.46558 0.47680 0.47474 0.45206 0.49404 0.49532 0.54349 0.52489 0.13357 0.00000 0.32255 0.36852 0.64537 0.81357 0.76208 0.75955 1.21456 Neurosp 0.83788 0.86446 0.84558 0.86301 0.84646 0.77286 0.79971 0.76948 0.78977 0.86847 0.87432 0.53453 0.53251 0.54124 0.51711 0.53405 0.49054 0.57662 0.49842 0.49593 0.50246 0.50367 0.48648 0.53472 0.51694 0.54724 0.54822 0.32481 0.32255 0.00000 0.42778 0.66131 0.83101 0.73069 0.74963 1.18679 Schizosac 0.87998 0.88854 0.88351 0.90678 0.89075 0.86205 0.84041 0.84372 0.84931 0.93244 0.97317 0.53799 0.53521 0.53667 0.48798 0.50747 0.49792 0.53073 0.44104 0.43198 0.44291 0.43906 0.45737 0.49236 0.47790 0.49884 0.50690 0.38180 0.36852 0.42778 0.00000 0.63895 0.82383 0.77399 0.79347 1.32319 Plasmodium 0.90840 0.90863 0.86703 0.97890 0.97510 0.89793 0.85154 0.90794 0.91523 0.91789 1.00427 0.55398 0.53993 0.55209 0.52774 0.55072 0.53326 0.55690 0.59522 0.58133 0.58310 0.57755 0.56408 0.59492 0.58731 0.55886 0.57208 0.66631 0.64537 0.66131 0.63895 0.00000 0.80551 0.80099 0.84272 1.24785 Giardia 1.00964 0.99885 0.98702 1.07954 1.05121 0.97445 0.93208 0.92046 0.92731 1.10539 1.09623 0.75997 0.74874 0.76955 0.75978 0.79064 0.73223 0.80548 0.81425 0.80389 0.81450 0.80015 0.76965 0.81238 0.80289 0.79901 0.78654 0.80997 0.81357 0.83101 0.82383 0.80551 0.00000 0.88335 0.90326 1.47385 Thermus 0.60166 0.63590 0.58902 0.63953 0.69758 0.55841 0.57636 0.56151 0.56141 0.73870 0.75630 0.75285 0.75984 0.76324 0.77302 0.80118 0.75080 0.76244 0.80686 0.78674 0.80084 0.77379 0.79702 0.85118 0.82046 0.75864 0.72814 0.76117 0.76208 0.73069 0.77399 0.80099 0.88335 0.00000 0.31346 1.23286 Deinococ 0.67490 0.71387 0.66908 0.72638 0.75993 0.66678 0.63266 0.61817 0.62670 0.82896 0.84000 0.79662 0.79772 0.79261 0.81680 0.82700 0.78263 0.80908 0.82796 0.81176 0.83018 0.80951 0.81526 0.84557 0.84892 0.80014 0.78839 0.74334 0.75955 0.74963 0.79347 0.84272 0.90326 0.31346 0.00000 1.17918 Borrelia 1.12338 1.18111 1.13905 1.12826 1.18175 1.09976 1.08603 0.99773 1.01885 1.13918 1.14451 1.26802 1.23484 1.24556 1.21904 1.24769 1.18616 1.20639 1.27939 1.25834 1.27329 1.24758 1.26523 1.33810 1.30611 1.24445 1.25526 1.23895 1.21456 1.18679 1.32319 1.24785 1.47385 1.23286 1.17918 0.00000 Average distance (over all possible pairs of sequences): 0.68981 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 0.27461 0.02620 37 0.35932 0.03149 MMethanos 2 0.31395 0.02817 38 0.26906 0.02598 Archaeogl 3 0.27836 0.02626 39 0.14483 0.02101 Haloferax 4 0.08880 0.01633 40 0.19497 0.02608 Halobact 5 0.12246 0.01802 41 0.13511 0.01879 jMethanoco 6 0.18606 0.02222 42 0.25318 0.02562 Methanobac 7 0.21158 0.02344 43 0.00167 0.00167 Desulfuroc 8 0.01442 0.00592 44 0.00950 0.00518 Thermococ 9 0.02236 0.00690 45 0.20306 0.02131 Enterococ 10 0.48960 0.03697 46 0.25263 0.02376 Sulfolobus 11 0.57889 0.04146 47 0.01127 0.00625 Daucus 12 0.02269 0.00642 48 0.26075 0.02416 Gossypium 13 0.02226 0.00639 49 0.01715 0.00739 Arabidopsi 14 0.03448 0.00844 50 0.19282 0.02092 '1Acetab' 15 0.00696 0.00475 51 0.41642 0.03662 '2Acetab' 16 0.04219 0.00881 52 0.17849 0.02594 Cyanidium 17 0.25459 0.02444 Trypanos 18 0.35419 0.02918 Homo 19 0.01772 0.00545 Bos 20 0.00195 0.00193 Mus 21 0.01603 0.00518 Gallus 22 0.02916 0.00750 Manduca 23 0.05000 0.01040 Aedes 24 0.07964 0.01251 Drosophila 25 0.08927 0.01318 Dictyost 26 0.29579 0.02595 Entamoeba 27 0.34279 0.02859 Saccharom 28 0.07336 0.01273 Candida 29 0.06212 0.01208 Neurosp 30 0.22597 0.02342 Schizosac 31 0.22786 0.02366 Plasmodium 32 0.42748 0.03290 Giardia 33 0.66215 0.04532 Thermus 34 0.12767 0.01950 Deinococ 35 0.19153 0.02269 7 iterations until convergence Borrelia 36 0.95334 0.06444 log L: -24452.34 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.27461,MMethanos:0.31395,Archaeogl:0.27836,Enterococ:0.48960, Sulfolobus:0.57889,Borrelia:0.95334,(Haloferax:0.08880,Halobact:0.12246) :0.35932,(Desulfuroc:0.01442,Thermococ:0.02236):0.26906,(jMethanoco:0.18606, Methanobac:0.21158):0.14483,((Thermus:0.12767,Deinococ:0.19153) :0.19497,(Giardia:0.66215,Trypanos:0.35419,Plasmodium:0.42748,Entamoeba:0.34279, Dictyost:0.29579,Cyanidium:0.25459,(Schizosac:0.22786,Neurosp:0.22597, (Saccharom:0.07336,Candida:0.06212):0.13511):0.25318,(Gallus:0.02916, (Mus:0.01603,(Homo:0.01772,Bos:0.00195):0.00167):0.00950):0.20306, ('1Acetab':0.00696,'2Acetab':0.04219):0.25263,(Arabidopsi:0.03448, (Daucus:0.02269,Gossypium:0.02226):0.01127):0.26075,(Manduca:0.05000, (Aedes:0.07964,Drosophila:0.08927):0.01715):0.19282):0.41642):0.17849); 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 0.27553 0.02630 37 0.36080 0.03158 MMethanos 2 0.31306 0.02814 38 0.26863 0.02592 Archaeogl 3 0.28016 0.02637 39 0.14463 0.02099 Haloferax 4 0.08872 0.01629 40 0.18863 0.02572 Halobact 5 0.12237 0.01801 41 0.13490 0.01879 jMethanoco 6 0.18404 0.02211 42 0.25508 0.02573 Methanobac 7 0.21337 0.02355 43 0.00167 0.00168 Desulfuroc 8 0.01464 0.00595 44 0.00977 0.00522 Thermococ 9 0.02214 0.00688 45 0.20058 0.02117 Enterococ 10 0.48643 0.03676 46 0.25277 0.02374 Sulfolobus 11 0.58087 0.04158 47 0.01133 0.00626 Daucus 12 0.02265 0.00642 48 0.25963 0.02411 Gossypium 13 0.02230 0.00640 49 0.01718 0.00741 Arabidopsi 14 0.03442 0.00844 50 0.19029 0.02078 '1Acetab' 15 0.00678 0.00471 51 0.17976 0.02744 '2Acetab' 16 0.04236 0.00882 52 0.26858 0.03224 Cyanidium 17 0.25440 0.02443 53 0.18099 0.02581 Trypanos 18 0.35428 0.02918 Homo 19 0.01772 0.00545 Bos 20 0.00195 0.00194 Mus 21 0.01603 0.00519 Gallus 22 0.02891 0.00748 Manduca 23 0.04988 0.01038 Aedes 24 0.07956 0.01251 Drosophila 25 0.08945 0.01320 Dictyost 26 0.29513 0.02592 Entamoeba 27 0.34190 0.02856 Saccharom 28 0.07335 0.01274 Candida 29 0.06211 0.01209 Neurosp 30 0.22668 0.02348 Schizosac 31 0.22739 0.02365 Plasmodium 32 0.42894 0.03298 Giardia 33 0.49405 0.04084 Thermus 34 0.12609 0.01930 Deinococ 35 0.19343 0.02271 8 iterations until convergence Borrelia 36 0.95367 0.06448 log L: -24414.62 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.27553,MMethanos:0.31306,Archaeogl:0.28016,Enterococ:0.48643, Sulfolobus:0.58087,Borrelia:0.95367,(Haloferax:0.08872,Halobact:0.12237) :0.36080,(Desulfuroc:0.01464,Thermococ:0.02214):0.26863,(jMethanoco:0.18404, Methanobac:0.21337):0.14463,((Thermus:0.12609,Deinococ:0.19343) :0.18863,(Giardia:0.49405,(Trypanos:0.35428,Plasmodium:0.42894,Entamoeba:0.34190, Dictyost:0.29513,Cyanidium:0.25440,(Schizosac:0.22739,Neurosp:0.22668, (Saccharom:0.07335,Candida:0.06211):0.13490):0.25508,(Gallus:0.02891, (Mus:0.01603,(Homo:0.01772,Bos:0.00195):0.00167):0.00977):0.20058, ('1Acetab':0.00678,'2Acetab':0.04236):0.25277,(Arabidopsi:0.03442, (Daucus:0.02265,Gossypium:0.02230):0.01133):0.25963,(Manduca:0.04988, (Aedes:0.07956,Drosophila:0.08945):0.01718):0.19029):0.17976):0.26858) :0.18099); 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 0.27631 0.02632 37 0.36116 0.03159 MMethanos 2 0.31493 0.02820 38 0.26844 0.02587 Archaeogl 3 0.28075 0.02640 39 0.14302 0.02085 Haloferax 4 0.08849 0.01631 40 0.18839 0.02550 Halobact 5 0.12269 0.01804 41 0.13406 0.01871 jMethanoco 6 0.18423 0.02211 42 0.25340 0.02568 Methanobac 7 0.21365 0.02356 43 0.00168 0.00168 Desulfuroc 8 0.01485 0.00597 44 0.00897 0.00502 Thermococ 9 0.02194 0.00685 45 0.19372 0.02084 Enterococ 10 0.48595 0.03670 46 0.25707 0.02397 Sulfolobus 11 0.57871 0.04142 47 0.01088 0.00614 Daucus 12 0.02253 0.00640 48 0.26125 0.02423 Gossypium 13 0.02241 0.00641 49 0.01674 0.00731 Arabidopsi 14 0.03477 0.00845 50 0.18320 0.02045 '1Acetab' 15 0.00656 0.00465 51 0.10531 0.01969 '2Acetab' 16 0.04255 0.00884 52 0.10635 0.02406 Cyanidium 17 0.25452 0.02449 53 0.25835 0.03147 Trypanos 18 0.26968 0.02684 54 0.18234 0.02575 Homo 19 0.01771 0.00545 Bos 20 0.00195 0.00194 Mus 21 0.01603 0.00519 Gallus 22 0.02967 0.00753 Manduca 23 0.05077 0.01048 Aedes 24 0.07983 0.01255 Drosophila 25 0.08906 0.01320 Dictyost 26 0.29593 0.02601 Entamoeba 27 0.33619 0.02832 Saccharom 28 0.07257 0.01271 Candida 29 0.06290 0.01216 Neurosp 30 0.22892 0.02357 Schizosac 31 0.22635 0.02361 Plasmodium 32 0.43338 0.03325 Giardia 33 0.50069 0.04067 Thermus 34 0.12657 0.01927 Deinococ 35 0.19195 0.02255 8 iterations until convergence Borrelia 36 0.95187 0.06437 log L: -24382.32 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.27631,MMethanos:0.31493,Archaeogl:0.28075,Enterococ:0.48595, Sulfolobus:0.57871,Borrelia:0.95187,(Haloferax:0.08849,Halobact:0.12269) :0.36116,(Desulfuroc:0.01485,Thermococ:0.02194):0.26844,(jMethanoco:0.18423, Methanobac:0.21365):0.14302,((Thermus:0.12657,Deinococ:0.19195) :0.18839,(Giardia:0.50069,(Trypanos:0.26968,(Plasmodium:0.43338, Entamoeba:0.33619,Dictyost:0.29593,Cyanidium:0.25452,(Schizosac:0.22635, Neurosp:0.22892,(Saccharom:0.07257,Candida:0.06290):0.13406):0.25340, (Gallus:0.02967,(Mus:0.01603,(Homo:0.01771,Bos:0.00195):0.00168):0.00897) :0.19372,('1Acetab':0.00656,'2Acetab':0.04255):0.25707,(Arabidopsi:0.03477, (Daucus:0.02253,Gossypium:0.02241):0.01088):0.26125,(Manduca:0.05077, (Aedes:0.07983,Drosophila:0.08906):0.01674):0.18320):0.10531):0.10635) :0.25835):0.18234); 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 0.27652 0.02631 37 0.36086 0.03155 MMethanos 2 0.31573 0.02822 38 0.26875 0.02586 Archaeogl 3 0.28053 0.02637 39 0.14243 0.02078 Haloferax 4 0.08844 0.01630 40 0.18946 0.02552 Halobact 5 0.12273 0.01804 41 0.14631 0.01899 jMethanoco 6 0.18393 0.02207 42 0.01811 0.00701 Methanobac 7 0.21378 0.02357 43 0.14252 0.01912 Desulfuroc 8 0.01486 0.00597 44 0.16332 0.02036 Thermococ 9 0.02193 0.00685 45 0.13101 0.01854 Enterococ 10 0.48526 0.03665 46 0.24795 0.02543 Sulfolobus 11 0.57898 0.04141 47 0.00168 0.00168 Daucus 12 0.02140 0.00624 48 0.00866 0.00486 Gossypium 13 0.02334 0.00649 49 0.17266 0.01963 Arabidopsi 14 0.02801 0.00798 50 0.01517 0.00694 '1Acetab' 15 0.01086 0.00569 51 0.16304 0.01927 '2Acetab' 16 0.03851 0.00860 52 0.11292 0.02026 Cyanidium 17 0.25765 0.02469 53 0.10421 0.02397 Trypanos 18 0.26920 0.02686 54 0.25992 0.03154 Homo 19 0.01771 0.00545 55 0.17958 0.02559 Bos 20 0.00195 0.00194 Mus 21 0.01603 0.00519 Gallus 22 0.02997 0.00752 Manduca 23 0.05321 0.01069 Aedes 24 0.08073 0.01264 Drosophila 25 0.08820 0.01318 Dictyost 26 0.28988 0.02567 Entamoeba 27 0.33677 0.02835 Saccharom 28 0.07335 0.01274 Candida 29 0.06197 0.01207 Neurosp 30 0.23146 0.02370 Schizosac 31 0.23025 0.02383 Plasmodium 32 0.44373 0.03370 Giardia 33 0.49773 0.04052 Thermus 34 0.12840 0.01938 Deinococ 35 0.19014 0.02247 10 iterations until convergence Borrelia 36 0.95132 0.06432 log L: -24266.16 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.27652,MMethanos:0.31573,Archaeogl:0.28053,Enterococ:0.48526, Sulfolobus:0.57898,Borrelia:0.95132,(Haloferax:0.08844,Halobact:0.12273) :0.36086,(Desulfuroc:0.01486,Thermococ:0.02193):0.26875,(jMethanoco:0.18393, Methanobac:0.21378):0.14243,((Thermus:0.12840,Deinococ:0.19014) :0.18946,(Giardia:0.49773,(Trypanos:0.26920,(Plasmodium:0.44373, Entamoeba:0.33677,Dictyost:0.28988,Cyanidium:0.25765,(('1Acetab':0.01086, '2Acetab':0.03851):0.14631,(Arabidopsi:0.02801,(Daucus:0.02140, Gossypium:0.02334):0.01811):0.14252):0.16332,(Schizosac:0.23025, Neurosp:0.23146,(Saccharom:0.07335,Candida:0.06197):0.13101):0.24795, (Gallus:0.02997,(Mus:0.01603,(Homo:0.01771,Bos:0.00195):0.00168):0.00866) :0.17266,(Manduca:0.05321,(Aedes:0.08073,Drosophila:0.08820):0.01517) :0.16304):0.11292):0.10421):0.25992):0.17958); 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 0.27652 0.02631 37 0.36063 0.03154 MMethanos 2 0.31574 0.02822 38 0.26883 0.02587 Archaeogl 3 0.28069 0.02638 39 0.14231 0.02077 Haloferax 4 0.08846 0.01629 40 0.18771 0.02541 Halobact 5 0.12268 0.01804 41 0.14906 0.01906 jMethanoco 6 0.18372 0.02205 42 0.01886 0.00721 Methanobac 7 0.21391 0.02357 43 0.13693 0.01873 Desulfuroc 8 0.01486 0.00598 44 0.08830 0.01677 Thermococ 9 0.02193 0.00685 45 0.11113 0.01807 Enterococ 10 0.48507 0.03664 46 0.12897 0.01842 Sulfolobus 11 0.57910 0.04141 47 0.24064 0.02512 Daucus 12 0.02153 0.00623 48 0.00168 0.00169 Gossypium 13 0.02372 0.00651 49 0.00934 0.00517 Arabidopsi 14 0.02678 0.00789 50 0.16497 0.01920 '1Acetab' 15 0.01390 0.00605 51 0.01413 0.00663 '2Acetab' 16 0.03556 0.00834 52 0.15396 0.01882 Cyanidium 17 0.18529 0.02159 53 0.11127 0.02017 Trypanos 18 0.27078 0.02698 54 0.10360 0.02395 Homo 19 0.01771 0.00545 55 0.25947 0.03151 Bos 20 0.00195 0.00195 56 0.18252 0.02576 Mus 21 0.01603 0.00519 Gallus 22 0.02929 0.00752 Manduca 23 0.05407 0.01071 Aedes 24 0.08102 0.01265 Drosophila 25 0.08800 0.01316 Dictyost 26 0.28946 0.02574 Entamoeba 27 0.32913 0.02808 Saccharom 28 0.07370 0.01273 Candida 29 0.06183 0.01204 Neurosp 30 0.23465 0.02387 Schizosac 31 0.22980 0.02378 Plasmodium 32 0.44723 0.03387 Giardia 33 0.49738 0.04054 Thermus 34 0.12703 0.01934 Deinococ 35 0.19119 0.02255 8 iterations until convergence Borrelia 36 0.95139 0.06432 log L: -24206.25 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (BMethanos:0.27652,MMethanos:0.31574,Archaeogl:0.28069,Enterococ:0.48507, Sulfolobus:0.57910,Borrelia:0.95139,(Haloferax:0.08846,Halobact:0.12268) :0.36063,(Desulfuroc:0.01486,Thermococ:0.02193):0.26883,(jMethanoco:0.18372, Methanobac:0.21391):0.14231,((Thermus:0.12703,Deinococ:0.19119) :0.18771,(Giardia:0.49738,(Trypanos:0.27078,(Plasmodium:0.44723, Entamoeba:0.32913,Dictyost:0.28946,(Cyanidium:0.18529,(('1Acetab':0.01390, '2Acetab':0.03556):0.14906,(Arabidopsi:0.02678,(Daucus:0.02153, Gossypium:0.02372):0.01886):0.13693):0.08830):0.11113,(Schizosac:0.22980, Neurosp:0.23465,(Saccharom:0.07370,Candida:0.06183):0.12897):0.24064, (Gallus:0.02929,(Mus:0.01603,(Homo:0.01771,Bos:0.00195):0.00168):0.00934) :0.16497,(Manduca:0.05407,(Aedes:0.08102,Drosophila:0.08800):0.01413) :0.15396):0.11127):0.10360):0.25947):0.18252); COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. Significantly worse -------------------------------------------------------- 1 -24452.34 246.09 33.60 yes 2 -24414.62 208.37 30.30 yes 3 -24382.32 176.07 27.86 yes 4 -24266.16 59.91 14.90 yes 5 -24206.25 0.00 <----------------- best tree This test (5% significance) follows Kishino and Hasegawa (1989). TIME STAMP Date and time: Tue May 28 23:08:53 2002 Runtime (excl. input) : 328 seconds (= 5.5 minutes = 0.1 hours) Runtime (incl. input) : 484 seconds (= 8.1 minutes = 0.1 hours)