TREE-PUZZLE 5.2 Input file name: atp_all.phy User tree file name: atpalltrees.txt Type of analysis: user tree evaluation Parameter estimation: accurate (slow) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 46 sequences with 780 amino acid sites Number of constant sites: 9 (= 1.2% of all sites) Number of site patterns: 728 Number of constant site patterns: 5 (= 0.7% of all site patterns) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 7.8% pi(R) = 5.9% pi(N) = 3.1% pi(D) = 5.7% pi(C) = 0.6% pi(Q) = 3.7% pi(E) = 7.8% pi(G) = 8.5% pi(H) = 1.3% pi(I) = 7.4% pi(L) = 8.9% pi(K) = 5.1% pi(M) = 2.6% pi(F) = 3.4% pi(P) = 5.2% pi(S) = 5.9% pi(T) = 5.6% pi(W) = 0.5% pi(Y) = 3.5% pi(V) = 7.7% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence BArabidops 0 288 288 36.92% BOryza 0 292 292 37.44% B_cyanidiu 0 280 280 35.90% BTrypanoso 0 295 295 37.82% BSaccharom 0 276 276 35.38% BEncephali 0 303 303 38.85% Bhomo 0 269 269 34.49% BCryptospo 0 287 287 36.79% BPlasmodiu 0 286 286 36.67% BPyrobacul 0 313 313 40.13% BSulfolo 0 315 315 40.38% B_halobact 0 309 309 39.62% BMacetiv 0 320 320 41.03% B_Mjanna 0 315 315 40.38% BGiardia 0 283 283 36.28% BNanoarcha 0 364 364 46.67% alphaAquif 0 277 277 35.51% alpha_Ther 0 307 307 39.36% alphaChlor 0 254 254 32.56% alphaEnter 0 262 262 33.59% alphaGeoba 0 277 277 35.51% alpha_Sacc 0 236 236 30.26% alpha_acet 0 247 247 31.67% F_Treponem 0 307 307 39.36% F_Bsubtili 0 354 354 45.38% F_Styphi 0 340 340 43.59% F_Borrelia 0 344 344 44.10% beta_Arabi 0 191 191 24.49% Beta_human 0 251 251 32.18% beta_Sacch 0 269 269 34.49% beta_Therm 0 309 309 39.62% beta_Enter 0 312 312 40.00% beta_aquif 0 302 302 38.72% beta_Cyani 0 290 290 37.18% beta_Macet 0 296 296 37.95% APyrobacul 0 187 187 23.97% ASulfolobu 0 188 188 24.10% A_Maceti 0 202 202 25.90% AHalobacte 0 195 195 25.00% AjMethanoc 0 186 186 23.85% AEnterococ 0 187 187 23.97% AArabidops 0 157 157 20.13% ACyanidium 0 193 193 24.74% A1Homo1_Ho 0 163 163 20.90% ASaccharom 0 163 163 20.90% AGiardia 0 126 126 16.15% ------------------------------------------------------- Sum 0 12167 12167 33.91% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 780 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value BArabidops passed 96.54% BOryza passed 98.65% B_cyanidiu passed 80.89% BTrypanoso passed 39.27% BSaccharom passed 75.87% BEncephali passed 62.22% Bhomo passed 57.18% BCryptospo passed 50.09% BPlasmodiu passed 5.30% BPyrobacul passed 16.66% BSulfolo passed 90.88% B_halobact failed 0.28% BMacetiv passed 98.62% B_Mjanna passed 91.23% BGiardia passed 5.02% BNanoarcha failed 0.00% alphaAquif passed 19.04% alpha_Ther passed 62.22% alphaChlor passed 59.60% alphaEnter passed 90.18% alphaGeoba passed 73.01% alpha_Sacc failed 0.20% alpha_acet passed 36.87% F_Treponem passed 79.80% F_Bsubtili passed 96.45% F_Styphi failed 0.36% F_Borrelia failed 0.00% beta_Arabi passed 41.59% Beta_human passed 10.78% beta_Sacch passed 67.77% beta_Therm passed 23.16% beta_Enter passed 76.32% beta_aquif passed 5.09% beta_Cyani passed 67.35% beta_Macet passed 71.68% APyrobacul failed 0.02% ASulfolobu failed 0.96% A_Maceti failed 4.99% AHalobacte failed 0.00% AjMethanoc failed 1.08% AEnterococ failed 1.28% AArabidops passed 55.33% ACyanidium passed 64.50% A1Homo1_Ho passed 31.11% ASaccharom passed 21.36% AGiardia failed 0.32% 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. 46 BArabidops 0.00000 0.05519 0.33171 0.43251 0.40878 0.37534 0.35372 0.40742 0.43087 1.10990 0.96356 0.88150 0.74592 0.78945 0.96910 1.39529 3.91742 3.76705 3.92693 4.21685 3.55603 4.32129 3.86643 4.76904 3.68209 3.98672 3.50929 4.05925 3.75835 3.58006 3.81456 3.70654 4.12673 3.89166 3.99385 5.76508 6.00719 5.45872 6.13420 5.71472 5.24973 5.88611 5.29215 5.42206 5.27396 5.71747 BOryza 0.05519 0.00000 0.31688 0.41511 0.38234 0.37684 0.34002 0.39644 0.40499 1.11134 0.97116 0.86598 0.74031 0.78133 0.95761 1.41208 3.92991 3.79734 4.00985 4.28404 3.57201 4.40191 3.94242 4.67003 3.67882 3.99342 3.48555 4.20024 3.84306 3.62295 3.90715 3.75390 4.26852 4.01982 3.96606 5.52605 5.64507 5.23964 5.94132 5.35692 5.04096 5.44871 5.12806 5.23929 4.98828 5.81569 B_cyanidiu 0.33171 0.31688 0.00000 0.41952 0.43191 0.44951 0.40832 0.43332 0.44422 1.11030 0.97590 0.90382 0.82333 0.81074 1.06808 1.36978 3.78563 3.78442 3.84497 4.18222 3.68332 4.25625 4.17938 4.66994 3.66892 3.85650 3.61841 4.25054 3.90885 3.72625 4.00395 4.03387 4.33573 4.05011 3.87965 5.55342 5.67179 5.29598 6.05092 5.62407 4.99761 6.07904 5.50656 5.66480 5.24283 5.79972 BTrypanoso 0.43251 0.41511 0.41952 0.00000 0.46600 0.48542 0.44871 0.58130 0.55301 1.18420 1.02564 0.96424 0.89985 0.93251 1.03073 1.48060 3.82131 3.80113 4.15468 4.02949 3.69973 4.44288 3.85939 4.71070 3.66577 3.97950 3.48926 4.31095 4.24177 3.81906 3.89756 3.86308 4.15991 4.25445 4.13229 5.93571 5.63244 5.41609 6.23528 5.43820 5.16265 5.73780 5.25483 5.78443 5.37536 6.00605 BSaccharom 0.40878 0.38234 0.43191 0.46600 0.00000 0.36064 0.38585 0.45680 0.47294 1.09214 1.00454 0.88536 0.78998 0.82869 1.07857 1.32747 3.93919 3.83285 3.90645 4.01964 3.72997 4.19818 4.27702 4.42248 3.32867 3.86831 3.33376 4.68515 4.50901 4.44187 4.50356 4.40694 4.68688 4.43457 4.22087 6.10652 5.84368 5.47657 5.70283 5.61418 5.28568 5.92853 5.27640 5.64088 5.54358 5.95223 BEncephali 0.37534 0.37684 0.44951 0.48542 0.36064 0.00000 0.39802 0.47746 0.47152 1.10653 1.00038 0.84975 0.80251 0.83060 0.99621 1.30322 3.98434 3.82784 4.01776 4.15814 3.79200 4.28675 4.03246 4.60747 3.73933 3.85116 3.49143 4.44334 4.13137 4.14620 3.96068 3.90965 4.52326 4.19361 4.34007 5.76551 6.05891 5.54345 5.54924 5.22537 5.41665 5.77403 5.17068 5.37894 5.23998 5.94086 Bhomo 0.35372 0.34002 0.40832 0.44871 0.38585 0.39802 0.00000 0.43458 0.45578 1.10295 1.04601 0.91814 0.86504 0.82069 1.07331 1.40165 4.19650 3.94907 4.20845 4.37294 3.82759 4.61828 4.18216 5.24042 3.93849 4.26341 3.83523 4.75271 4.43308 4.46111 4.16987 4.34389 4.71012 4.56361 4.55984 6.04076 5.73474 5.72033 6.30613 5.80366 5.63248 6.02812 5.72267 5.84908 5.53925 6.44834 BCryptospo 0.40742 0.39644 0.43332 0.58130 0.45680 0.47746 0.43458 0.00000 0.28871 1.14976 0.92565 0.87421 0.78021 0.78944 1.07671 1.43746 4.01851 4.01233 4.13100 4.17078 3.99910 4.49686 4.18955 4.76974 3.44565 3.81965 3.54940 4.49467 4.28619 4.04230 4.53754 4.26380 4.60878 4.20175 4.18581 5.97502 5.91822 5.69741 6.10608 5.97711 5.43540 6.09245 5.23047 5.55360 5.61594 6.18433 BPlasmodiu 0.43087 0.40499 0.44422 0.55301 0.47294 0.47152 0.45578 0.28871 0.00000 1.16088 0.94501 0.90372 0.81226 0.83619 1.06588 1.46290 4.19071 4.07130 4.24387 4.37326 3.96337 4.59068 4.28630 4.52055 3.67009 3.99698 3.47606 4.52881 4.33835 4.13019 4.46470 4.03996 4.57795 4.12829 4.07792 5.83919 6.13769 5.60774 6.08064 5.66985 5.42725 5.80376 5.27050 5.62953 5.40526 5.81735 BPyrobacul 1.10990 1.11134 1.11030 1.18420 1.09214 1.10653 1.10295 1.14976 1.16088 0.00000 0.90464 0.97379 0.91726 0.76181 1.22654 1.39803 3.95525 3.66289 4.23155 3.90125 3.75439 4.57631 4.05453 4.29082 3.52681 3.93212 3.60237 5.09520 4.62078 4.54702 4.47869 4.50233 4.72981 4.71509 4.12511 4.82820 4.90498 4.98389 5.06029 4.47924 4.54500 5.41700 5.27878 4.94636 4.91308 5.06889 BSulfolo 0.96356 0.97116 0.97590 1.02564 1.00454 1.00038 1.04601 0.92565 0.94501 0.90464 0.00000 0.87718 0.80479 0.71374 1.24884 1.33970 3.64209 3.55976 3.87031 3.84399 3.79490 3.91457 3.55151 4.29343 3.40865 4.01087 3.28349 3.99394 3.71935 3.49168 3.92702 3.64902 4.28519 3.48080 3.80192 5.37668 5.30914 5.22511 5.38244 4.69067 4.50819 5.39267 4.91789 4.91149 5.11967 5.71852 B_halobact 0.88150 0.86598 0.90382 0.96424 0.88536 0.84975 0.91814 0.87421 0.90372 0.97379 0.87718 0.00000 0.52375 0.63657 1.21201 1.40850 3.67556 3.86574 3.88479 3.98066 3.86397 3.93160 3.79026 4.00321 3.23228 3.58743 3.39672 4.25843 4.19792 4.10943 4.03057 3.85552 4.68625 4.16920 3.97201 4.71728 4.90226 4.84213 4.79935 4.42517 4.49962 5.62993 5.38220 5.26411 5.18400 5.72040 BMacetiv 0.74592 0.74031 0.82333 0.89985 0.78998 0.80251 0.86504 0.78021 0.81226 0.91726 0.80479 0.52375 0.00000 0.51152 1.04718 1.31570 3.85251 3.82253 3.95778 4.09646 3.99109 4.18933 3.96461 4.00124 3.24481 3.68789 3.41595 4.20478 4.23354 4.05631 4.06073 3.86000 4.61833 4.33310 4.30272 4.83761 4.60981 4.71879 5.20616 4.75680 4.95974 5.15207 5.09222 4.74748 4.86255 5.34064 B_Mjanna 0.78945 0.78133 0.81074 0.93251 0.82869 0.83060 0.82069 0.78944 0.83619 0.76181 0.71374 0.63657 0.51152 0.00000 1.04167 1.17385 3.62368 3.52938 3.62950 3.55832 3.71632 4.13741 3.77973 4.07525 3.22394 3.49683 3.28440 4.29192 4.12327 4.15738 3.89197 4.01913 4.35935 4.01122 3.85584 5.06131 5.53405 5.19927 5.17201 4.86252 4.89772 5.68022 5.63036 5.39114 5.46720 5.58601 BGiardia 0.96910 0.95761 1.06808 1.03073 1.07857 0.99621 1.07331 1.07671 1.06588 1.22654 1.24884 1.21201 1.04718 1.04167 0.00000 1.62099 4.19913 3.96791 4.20763 3.96388 3.85800 4.11582 3.77083 4.71262 3.43399 3.83569 3.75786 4.44176 4.44907 4.09710 4.10367 3.94158 4.49010 4.41236 3.98878 5.41988 5.37692 5.30008 5.41108 5.21235 4.78252 5.77901 5.41483 5.54978 5.42375 5.17669 BNanoarcha 1.39529 1.41208 1.36978 1.48060 1.32747 1.30322 1.40165 1.43746 1.46290 1.39803 1.33970 1.40850 1.31570 1.17385 1.62099 0.00000 4.42708 3.93777 4.45656 4.10614 4.26816 4.66213 4.52085 4.15901 3.66990 4.33247 3.55351 3.61807 3.57162 3.74595 3.71407 3.54500 3.96288 3.62781 3.31377 4.48159 5.05690 5.18980 5.17428 5.12886 4.83347 5.46146 4.90552 4.95441 5.19131 4.91586 alphaAquif 3.91742 3.92991 3.78563 3.82131 3.93919 3.98434 4.19650 4.01851 4.19071 3.95525 3.64209 3.67556 3.85251 3.62368 4.19913 4.42708 0.00000 0.46719 0.62283 0.65940 0.55102 0.73109 1.15188 3.99772 3.08055 3.98113 3.66780 4.63732 4.70989 4.34147 4.47810 4.51418 4.51543 4.62394 4.19951 5.94707 6.71191 6.57990 5.73079 6.76396 5.97240 7.43616 7.02847 7.11948 6.87714 6.97845 alpha_Ther 3.76705 3.79734 3.78442 3.80113 3.83285 3.82784 3.94907 4.01233 4.07130 3.66289 3.55976 3.86574 3.82253 3.52938 3.96791 3.93777 0.46719 0.00000 0.51793 0.58214 0.51897 0.72348 1.00731 4.14069 3.35876 4.41937 3.75135 4.71832 4.51045 4.38397 4.62662 4.74738 4.30755 4.85345 4.54564 5.49029 6.84144 6.31825 5.51883 6.34126 5.72087 6.54321 6.51227 6.75370 6.71423 6.64659 alphaChlor 3.92693 4.00985 3.84497 4.15468 3.90645 4.01776 4.20845 4.13100 4.24387 4.23155 3.87031 3.88479 3.95778 3.62950 4.20763 4.45656 0.62283 0.51793 0.00000 0.68090 0.52950 0.64283 1.17213 3.83625 3.36161 3.98572 3.65055 4.42381 4.46326 4.46221 4.49307 4.53423 4.43115 4.58420 4.34235 5.12926 6.40834 5.92810 5.26050 6.22411 5.31551 6.93823 6.50916 6.35315 5.93401 6.43068 alphaEnter 4.21685 4.28404 4.18222 4.02949 4.01964 4.15814 4.37294 4.17078 4.37326 3.90125 3.84399 3.98066 4.09646 3.55832 3.96388 4.10614 0.65940 0.58214 0.68090 0.00000 0.53076 0.81035 1.17155 4.00174 3.10709 3.72656 3.82432 4.76644 4.76058 4.64879 4.66928 4.72042 4.73800 4.84667 4.79042 6.20968 7.23457 6.47377 5.72298 7.18464 6.03550 8.25418 7.19197 7.37273 7.38617 7.40109 alphaGeoba 3.55603 3.57201 3.68332 3.69973 3.72997 3.79200 3.82759 3.99910 3.96337 3.75439 3.79490 3.86397 3.99109 3.71632 3.85800 4.26816 0.55102 0.51897 0.52950 0.53076 0.00000 0.63853 1.25866 3.73324 3.09689 3.90078 3.55005 4.52657 4.17258 4.11899 4.19233 4.32346 4.12498 4.71191 4.19505 5.68553 6.14552 5.34981 5.33766 5.76240 5.08850 6.90145 6.15384 5.88370 6.02012 6.09035 alpha_Sacc 4.32129 4.40191 4.25625 4.44288 4.19818 4.28675 4.61828 4.49686 4.59068 4.57631 3.91457 3.93160 4.18933 4.13741 4.11582 4.66213 0.73109 0.72348 0.64283 0.81035 0.63853 0.00000 1.31977 3.63033 3.12993 3.85297 3.35616 4.66023 4.72507 4.36509 4.58858 4.57450 4.37319 4.79753 4.66573 5.68904 6.27701 5.89225 5.41894 5.81592 5.14387 6.69814 6.14543 6.55961 5.91105 6.26855 alpha_acet 3.86643 3.94242 4.17938 3.85939 4.27702 4.03246 4.18216 4.18955 4.28630 4.05453 3.55151 3.79026 3.96461 3.77973 3.77083 4.52085 1.15188 1.00731 1.17213 1.17155 1.25866 1.31977 0.00000 4.04387 3.16442 3.69206 3.57833 4.64227 4.57763 4.21279 3.91950 4.53475 4.22404 4.47229 4.44601 6.72743 7.45752 7.35637 6.67447 7.34618 6.31476 8.18965 7.88318 7.93713 7.41199 7.66838 F_Treponem 4.76904 4.67003 4.66994 4.71070 4.42248 4.60747 5.24042 4.76974 4.52055 4.29082 4.29343 4.00321 4.00124 4.07525 4.71262 4.15901 3.99772 4.14069 3.83625 4.00174 3.73324 3.63033 4.04387 0.00000 0.79108 1.31432 1.23999 3.48290 3.48916 3.50983 3.26321 3.50361 3.46286 3.63838 3.58847 4.36514 4.71959 4.45303 4.25512 4.04161 4.39329 4.92662 4.67880 4.77957 4.44984 4.55048 F_Bsubtili 3.68209 3.67882 3.66892 3.66577 3.32867 3.73933 3.93849 3.44565 3.67009 3.52681 3.40865 3.23228 3.24481 3.22394 3.43399 3.66990 3.08055 3.35876 3.36161 3.10709 3.09689 3.12993 3.16442 0.79108 0.00000 1.08495 1.21311 2.90216 2.81109 2.68984 2.77963 2.93995 3.01341 3.02598 2.93263 4.22968 4.70949 4.06142 4.22255 4.18973 4.18541 4.28482 4.00860 4.16027 4.21423 4.35160 F_Styphi 3.98672 3.99342 3.85650 3.97950 3.86831 3.85116 4.26341 3.81965 3.99698 3.93212 4.01087 3.58743 3.68789 3.49683 3.83569 4.33247 3.98113 4.41937 3.98572 3.72656 3.90078 3.85297 3.69206 1.31432 1.08495 0.00000 1.45220 3.23424 3.08199 3.17775 3.22517 3.11346 3.16551 3.20319 2.97834 4.46568 5.14988 4.71218 4.93065 5.00227 5.04625 4.90850 4.72839 4.49861 4.46001 4.69399 F_Borrelia 3.50929 3.48555 3.61841 3.48926 3.33376 3.49143 3.83523 3.54940 3.47606 3.60237 3.28349 3.39672 3.41595 3.28440 3.75786 3.55351 3.66780 3.75135 3.65055 3.82432 3.55005 3.35616 3.57833 1.23999 1.21311 1.45220 0.00000 2.92287 2.85764 2.78605 3.09831 2.62763 2.82580 3.01705 3.08160 4.44425 4.66871 4.18979 3.98603 4.54990 4.10579 4.34208 4.20818 4.21326 4.24506 4.38910 beta_Arabi 4.05925 4.20024 4.25054 4.31095 4.68515 4.44334 4.75271 4.49467 4.52881 5.09520 3.99394 4.25843 4.20478 4.29192 4.44176 3.61807 4.63732 4.71832 4.42381 4.76644 4.52657 4.66023 4.64227 3.48290 2.90216 3.23424 2.92287 0.00000 0.35750 0.40320 0.52835 0.56322 0.64703 0.61649 1.10167 4.35379 4.52450 4.08128 4.25332 4.53720 4.29398 4.66636 4.27412 4.73677 4.71375 4.29483 Beta_human 3.75835 3.84306 3.90885 4.24177 4.50901 4.13137 4.43308 4.28619 4.33835 4.62078 3.71935 4.19792 4.23354 4.12327 4.44907 3.57162 4.70989 4.51045 4.46326 4.76058 4.17258 4.72507 4.57763 3.48916 2.81109 3.08199 2.85764 0.35750 0.00000 0.35155 0.47987 0.52601 0.56763 0.57753 1.11846 3.89403 4.27700 4.13287 4.25416 4.28669 4.03720 4.53403 3.89968 4.38407 4.54126 4.03281 beta_Sacch 3.58006 3.62295 3.72625 3.81906 4.44187 4.14620 4.46111 4.04230 4.13019 4.54702 3.49168 4.10943 4.05631 4.15738 4.09710 3.74595 4.34147 4.38397 4.46221 4.64879 4.11899 4.36509 4.21279 3.50983 2.68984 3.17775 2.78605 0.40320 0.35155 0.00000 0.54079 0.52047 0.56680 0.57318 1.06030 3.82012 4.00187 3.81576 4.15812 3.96213 3.95339 3.82586 3.60904 3.97317 4.16898 3.98497 beta_Therm 3.81456 3.90715 4.00395 3.89756 4.50356 3.96068 4.16987 4.53754 4.46470 4.47869 3.92702 4.03057 4.06073 3.89197 4.10367 3.71407 4.47810 4.62662 4.49307 4.66928 4.19233 4.58858 3.91950 3.26321 2.77963 3.22517 3.09831 0.52835 0.47987 0.54079 0.00000 0.51618 0.54367 0.59662 1.00216 3.61433 4.13712 4.07621 3.93916 4.23414 4.09696 4.12105 3.93029 4.29083 4.28451 4.10607 beta_Enter 3.70654 3.75390 4.03387 3.86308 4.40694 3.90965 4.34389 4.26380 4.03996 4.50233 3.64902 3.85552 3.86000 4.01913 3.94158 3.54500 4.51418 4.74738 4.53423 4.72042 4.32346 4.57450 4.53475 3.50361 2.93995 3.11346 2.62763 0.56322 0.52601 0.52047 0.51618 0.00000 0.59683 0.59742 1.04684 3.91965 4.27193 3.74470 3.91966 3.81197 4.00209 3.85679 3.76802 4.05139 4.18665 3.95923 beta_aquif 4.12673 4.26852 4.33573 4.15991 4.68688 4.52326 4.71012 4.60878 4.57795 4.72981 4.28519 4.68625 4.61833 4.35935 4.49010 3.96288 4.51543 4.30755 4.43115 4.73800 4.12498 4.37319 4.22404 3.46286 3.01341 3.16551 2.82580 0.64703 0.56763 0.56680 0.54367 0.59683 0.00000 0.62978 0.95640 3.85441 4.29338 3.99250 4.30392 4.36053 3.96245 4.36908 4.23981 4.48132 4.44744 4.18473 beta_Cyani 3.89166 4.01982 4.05011 4.25445 4.43457 4.19361 4.56361 4.20175 4.12829 4.71509 3.48080 4.16920 4.33310 4.01122 4.41236 3.62781 4.62394 4.85345 4.58420 4.84667 4.71191 4.79753 4.47229 3.63838 3.02598 3.20319 3.01705 0.61649 0.57753 0.57318 0.59662 0.59742 0.62978 0.00000 0.95453 4.31667 4.58399 4.19599 4.61650 4.59522 4.46735 4.19406 3.94207 4.20964 4.55960 4.23316 beta_Macet 3.99385 3.96606 3.87965 4.13229 4.22087 4.34007 4.55984 4.18581 4.07792 4.12511 3.80192 3.97201 4.30272 3.85584 3.98878 3.31377 4.19951 4.54564 4.34235 4.79042 4.19505 4.66573 4.44601 3.58847 2.93263 2.97834 3.08160 1.10167 1.11846 1.06030 1.00216 1.04684 0.95640 0.95453 0.00000 4.19542 4.53310 4.46663 4.70379 4.82772 4.25522 4.66693 4.29019 4.67521 4.67755 4.48348 APyrobacul 5.76508 5.52605 5.55342 5.93571 6.10652 5.76551 6.04076 5.97502 5.83919 4.82820 5.37668 4.71728 4.83761 5.06131 5.41988 4.48159 5.94707 5.49029 5.12926 6.20968 5.68553 5.68904 6.72743 4.36514 4.22968 4.46568 4.44425 4.35379 3.89403 3.82012 3.61433 3.91965 3.85441 4.31667 4.19542 0.00000 0.91556 1.19877 1.22984 1.07668 1.34852 1.53631 1.38113 1.56396 1.40535 1.66915 ASulfolobu 6.00719 5.64507 5.67179 5.63244 5.84368 6.05891 5.73474 5.91822 6.13769 4.90498 5.30914 4.90226 4.60981 5.53405 5.37692 5.05690 6.71191 6.84144 6.40834 7.23457 6.14552 6.27701 7.45752 4.71959 4.70949 5.14988 4.66871 4.52450 4.27700 4.00187 4.13712 4.27193 4.29338 4.58399 4.53310 0.91556 0.00000 1.14049 1.15352 0.91713 1.12369 1.23386 1.15565 1.30029 1.23726 1.47284 A_Maceti 5.45872 5.23964 5.29598 5.41609 5.47657 5.54345 5.72033 5.69741 5.60774 4.98389 5.22511 4.84213 4.71879 5.19927 5.30008 5.18980 6.57990 6.31825 5.92810 6.47377 5.34981 5.89225 7.35637 4.45303 4.06142 4.71218 4.18979 4.08128 4.13287 3.81576 4.07621 3.74470 3.99250 4.19599 4.46663 1.19877 1.14049 0.00000 0.67885 0.73421 0.95212 1.12069 0.99275 1.14021 1.19859 1.36858 AHalobacte 6.13420 5.94132 6.05092 6.23528 5.70283 5.54924 6.30613 6.10608 6.08064 5.06029 5.38244 4.79935 5.20616 5.17201 5.41108 5.17428 5.73079 5.51883 5.26050 5.72298 5.33766 5.41894 6.67447 4.25512 4.22255 4.93065 3.98603 4.25332 4.25416 4.15812 3.93916 3.91966 4.30392 4.61650 4.70379 1.22984 1.15352 0.67885 0.00000 0.79315 0.89072 1.22494 1.09130 1.20618 1.27403 1.42470 AjMethanoc 5.71472 5.35692 5.62407 5.43820 5.61418 5.22537 5.80366 5.97711 5.66985 4.47924 4.69067 4.42517 4.75680 4.86252 5.21235 5.12886 6.76396 6.34126 6.22411 7.18464 5.76240 5.81592 7.34618 4.04161 4.18973 5.00227 4.54990 4.53720 4.28669 3.96213 4.23414 3.81197 4.36053 4.59522 4.82772 1.07668 0.91713 0.73421 0.79315 0.00000 0.73434 1.07665 0.95622 1.04903 1.09305 1.32602 AEnterococ 5.24973 5.04096 4.99761 5.16265 5.28568 5.41665 5.63248 5.43540 5.42725 4.54500 4.50819 4.49962 4.95974 4.89772 4.78252 4.83347 5.97240 5.72087 5.31551 6.03550 5.08850 5.14387 6.31476 4.39329 4.18541 5.04625 4.10579 4.29398 4.03720 3.95339 4.09696 4.00209 3.96245 4.46735 4.25522 1.34852 1.12369 0.95212 0.89072 0.73434 0.00000 1.27815 1.05444 1.18069 1.20598 1.58111 AArabidops 5.88611 5.44871 6.07904 5.73780 5.92853 5.77403 6.02812 6.09245 5.80376 5.41700 5.39267 5.62993 5.15207 5.68022 5.77901 5.46146 7.43616 6.54321 6.93823 8.25418 6.90145 6.69814 8.18965 4.92662 4.28482 4.90850 4.34208 4.66636 4.53403 3.82586 4.12105 3.85679 4.36908 4.19406 4.66693 1.53631 1.23386 1.12069 1.22494 1.07665 1.27815 0.00000 0.41209 0.50545 0.68471 1.03816 ACyanidium 5.29215 5.12806 5.50656 5.25483 5.27640 5.17068 5.72267 5.23047 5.27050 5.27878 4.91789 5.38220 5.09222 5.63036 5.41483 4.90552 7.02847 6.51227 6.50916 7.19197 6.15384 6.14543 7.88318 4.67880 4.00860 4.72839 4.20818 4.27412 3.89968 3.60904 3.93029 3.76802 4.23981 3.94207 4.29019 1.38113 1.15565 0.99275 1.09130 0.95622 1.05444 0.41209 0.00000 0.44055 0.61827 0.91052 A1Homo1_Ho 5.42206 5.23929 5.66480 5.78443 5.64088 5.37894 5.84908 5.55360 5.62953 4.94636 4.91149 5.26411 4.74748 5.39114 5.54978 4.95441 7.11948 6.75370 6.35315 7.37273 5.88370 6.55961 7.93713 4.77957 4.16027 4.49861 4.21326 4.73677 4.38407 3.97317 4.29083 4.05139 4.48132 4.20964 4.67521 1.56396 1.30029 1.14021 1.20618 1.04903 1.18069 0.50545 0.44055 0.00000 0.56766 1.07932 ASaccharom 5.27396 4.98828 5.24283 5.37536 5.54358 5.23998 5.53925 5.61594 5.40526 4.91308 5.11967 5.18400 4.86255 5.46720 5.42375 5.19131 6.87714 6.71423 5.93401 7.38617 6.02012 5.91105 7.41199 4.44984 4.21423 4.46001 4.24506 4.71375 4.54126 4.16898 4.28451 4.18665 4.44744 4.55960 4.67755 1.40535 1.23726 1.19859 1.27403 1.09305 1.20598 0.68471 0.61827 0.56766 0.00000 1.11060 AGiardia 5.71747 5.81569 5.79972 6.00605 5.95223 5.94086 6.44834 6.18433 5.81735 5.06889 5.71852 5.72040 5.34064 5.58601 5.17669 4.91586 6.97845 6.64659 6.43068 7.40109 6.09035 6.26855 7.66838 4.55048 4.35160 4.69399 4.38910 4.29483 4.03281 3.98497 4.10607 3.95923 4.18473 4.23316 4.48348 1.66915 1.47284 1.36858 1.42470 1.32602 1.58111 1.03816 0.91052 1.07932 1.11060 0.00000 Average distance (over all possible pairs of sequences): 3.76850 minimum : 0.05519, maximum : 8.25418 variance : 3.10906, std.dev. : 1.76325 RATE HETEROGENEITY Model of rate heterogeneity: mixed (1 invariable + 8 Gamma rates) Fraction of invariable sites (estimated from data set): 0.01 (S.E. 0.00) Number of invariable sites: 6 Gamma distribution parameter alpha (estimated from data set): 1.44 (S.E. 0.08) Number of Gamma rate categories: 8 Total rate heterogeneity (invariable sites + Gamma model): 0.41 (S.E. 0.02) Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 0 0.0000 0.0082 1 0.1388 0.1240 2 0.3247 0.1240 3 0.5063 0.1240 4 0.7049 0.1240 5 0.9382 0.1240 6 1.2350 0.1240 7 1.6662 0.1240 8 2.5520 0.1240 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.69. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming NJ tree): 1 1 1 1 1 4 6 6 8 1 1 8 1 8 8 6 1 1 1 1 8 1 8 6 4 1 4 4 6 1 8 1 6 1 1 6 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 2 8 8 8 6 8 8 6 8 8 8 8 8 7 6 8 8 8 8 8 8 5 8 8 8 8 8 8 4 8 7 8 5 8 6 8 8 5 7 7 6 7 5 7 5 8 8 5 8 7 7 6 4 8 6 7 8 8 4 7 7 8 8 4 5 2 3 3 5 7 2 5 2 3 4 2 4 2 6 4 4 6 7 5 7 4 6 4 3 4 4 4 5 8 6 4 4 8 7 5 6 2 4 2 4 3 5 7 5 7 7 2 5 4 2 3 2 2 4 2 5 4 6 5 7 4 6 5 7 4 7 2 6 2 4 6 5 3 5 7 1 8 4 6 6 4 2 6 2 6 5 8 8 4 8 3 6 5 8 5 1 8 7 8 2 2 8 4 5 4 1 1 2 5 2 4 3 3 5 2 8 6 4 8 7 1 6 3 6 7 2 6 8 8 8 7 6 8 8 1 4 1 1 1 8 1 8 4 8 6 6 8 8 5 7 7 2 8 4 2 3 2 5 4 3 6 4 8 6 7 7 8 8 4 8 1 7 8 8 7 4 2 8 4 8 3 3 3 3 8 3 3 3 4 7 7 1 5 5 3 7 5 3 3 4 1 0 2 1 3 1 1 3 3 3 1 3 4 3 0 1 1 3 2 2 2 1 2 2 1 1 1 1 1 3 3 3 3 2 1 2 3 1 2 3 5 4 5 6 3 8 8 8 8 6 2 8 8 8 8 5 8 8 7 7 6 3 6 2 1 2 2 2 2 0 1 1 4 1 2 2 5 4 3 4 8 5 2 4 4 3 3 2 4 7 5 4 8 1 1 8 4 8 8 8 8 8 1 4 1 8 8 7 7 5 4 5 1 2 5 3 2 5 1 2 1 1 2 1 2 3 2 1 4 4 1 2 3 3 1 3 1 5 1 0 2 1 1 2 6 5 3 5 2 1 2 2 4 3 1 1 2 1 1 3 2 2 1 2 1 1 2 1 3 2 2 3 1 2 0 2 1 2 1 2 1 2 1 2 4 2 3 2 2 4 2 2 0 0 1 1 4 3 7 4 4 7 6 5 7 2 6 8 1 7 8 7 8 8 8 7 2 8 8 6 1 8 8 1 8 8 8 6 6 8 4 8 8 6 1 8 1 1 2 1 2 3 2 2 1 1 1 2 2 1 1 4 1 1 2 1 1 2 2 2 2 2 1 1 1 2 1 1 3 1 3 3 7 2 3 5 5 2 3 3 0 1 2 2 2 2 5 1 2 0 3 4 5 6 5 5 3 5 5 6 4 2 2 8 6 6 3 2 6 7 4 2 5 5 3 4 5 6 1 2 6 4 6 4 4 5 2 2 2 3 2 2 1 6 4 3 2 2 5 6 5 5 4 7 4 1 6 2 2 4 6 3 3 5 6 6 3 3 6 1 4 7 5 5 7 3 2 5 5 5 3 6 6 5 5 6 7 7 3 5 7 5 4 7 7 6 6 8 6 5 7 7 7 8 7 6 7 7 7 8 8 8 8 8 7 7 8 8 5 8 8 6 6 8 5 7 8 7 8 8 6 4 7 6 8 8 8 8 8 8 7 8 8 2 8 8 8 8 8 6 8 8 7 4 5 8 8 7 4 8 8 8 7 8 8 6 8 8 8 8 8 1 6 6 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. :--41 AEnterococ :------------79 : : :---46 AGiardia : : :--73 : : : : :--45 ASaccharom : : : :-72 : : : : :-43 ACyanidium : : : :-71 : : : : :-42 AArabidops : : : :-70 : : : :-44 A1Homo1_Ho : :-78 : : :---36 APyrobacul : : :--74 : : : :--37 ASulfolobu : :-77 : : :-40 AjMethanoc : :-76 : : :--39 AHalobacte : :-75 : :--38 A_Maceti :-86 : : :---23 alpha_acet : :----------85 : : :-21 alphaGeoba : :--84 : : :--22 alpha_Sacc : : :-80 : : : :-19 alphaChlor : :-83 : : :--17 alphaAquif : :-82 : : :--20 alphaEnter : :-81 : :--18 alpha_Ther : : :---27 F_Borrelia :------89 : : :----26 F_Styphi : :--88 : : :--25 F_Bsubtili : :-87 : :---24 F_Treponem : : :---35 beta_Macet : :-----53 : : : :--32 beta_Enter : : :--52 : : : :--31 beta_Therm : : :-51 : : : :--34 beta_Cyani : : :-50 : : : :-30 beta_Sacch : : :-49 : : : :--33 beta_aquif : : :-48 : : : :-28 beta_Arabi : : :-47 : : :-29 Beta_human :-69 : :----16 BNanoarcha :--------68 : :--11 BSulfolo :--67 : :---10 BPyrobacul :-66 : :-14 B_Mjanna :-65 : :--12 B_halobact : :-54 : : :--13 BMacetiv :-64 : :---15 BGiardia :-63 : :-8 BCryptospo : :-55 : : :-9 BPlasmodiu :--62 : :-7 Bhomo : :-57 : : : :-6 BEncephali : : :-56 : : :-5 BSaccharom :-61 : :-3 B_cyanidiu : :-58 : : :--4 BTrypanoso :-60 : :-1 BArabidops :-59 :-2 BOryza branch length S.E. branch length S.E. BArabidops 1 0.04778 0.01381 47 0.11395 0.02777 BOryza 2 0.02982 0.01188 48 0.00602 0.01185 B_cyanidiu 3 0.23165 0.03310 49 0.13463 0.03150 BTrypanoso 4 0.39553 0.04366 50 0.07190 0.02594 BSaccharom 5 0.22234 0.03286 51 0.05904 0.03191 BEncephali 6 0.30632 0.03837 52 0.47335 0.08414 Bhomo 7 0.25809 0.03337 53 1.47507 0.20921 BCryptospo 8 0.18052 0.02865 54 0.17468 0.03906 BPlasmodiu 9 0.21997 0.03110 55 0.08453 0.02634 BPyrobacul 10 0.72444 0.07357 56 0.09214 0.02503 BSulfolo 11 0.49283 0.06331 57 0.03659 0.01716 B_halobact 12 0.45339 0.05436 58 0.05477 0.02129 BMacetiv 13 0.32013 0.04627 59 0.19015 0.02983 B_Mjanna 14 0.30219 0.04514 60 0.05637 0.02045 BGiardia 15 0.90412 0.08702 61 0.11585 0.02746 BNanoarcha 16 1.10083 0.13006 62 0.35264 0.05562 alphaAquif 17 0.37804 0.04303 63 0.28474 0.05278 alpha_Ther 18 0.32298 0.04160 64 0.05506 0.02963 alphaChlor 19 0.28009 0.03911 65 0.12327 0.03817 alphaEnter 20 0.43585 0.04710 66 0.09527 0.04455 alphaGeoba 21 0.30147 0.03901 67 0.37432 0.10416 alpha_Sacc 22 0.54777 0.05543 68 2.24050 0.28374 alpha_acet 23 0.72060 0.09776 69 0.00001 0.00034 F_Treponem 24 0.69823 0.08410 70 0.02873 0.01702 F_Bsubtili 25 0.52497 0.07620 71 0.08319 0.02690 F_Styphi 26 1.06720 0.11358 72 0.17949 0.04032 F_Borrelia 27 0.81674 0.11296 73 0.49267 0.05785 beta_Arabi 28 0.24846 0.03194 74 0.36319 0.05071 Beta_human 29 0.19277 0.02869 75 0.22892 0.03769 beta_Sacch 30 0.25615 0.03483 76 0.05385 0.02480 beta_Therm 31 0.33220 0.04292 77 0.02413 0.02562 beta_Enter 32 0.35781 0.04626 78 0.13311 0.05000 beta_aquif 33 0.56410 0.05658 79 3.48152 0.38132 beta_Cyani 34 0.44440 0.04873 80 0.15091 0.03343 beta_Macet 35 0.66341 0.08800 81 0.05263 0.02127 APyrobacul 36 0.64845 0.06287 82 0.03479 0.02076 ASulfolobu 37 0.42982 0.05101 83 0.01858 0.02088 A_Maceti 38 0.38205 0.04348 84 0.57819 0.09619 AHalobacte 39 0.42489 0.04630 85 2.93817 0.34411 AjMethanoc 40 0.27372 0.03623 86 0.00001 0.00032 AEnterococ 41 0.44162 0.05347 87 0.18126 0.06954 AArabidops 42 0.30340 0.03277 88 0.37301 0.09965 ACyanidium 43 0.23691 0.02973 89 1.56984 0.22276 A1Homo1_Ho 44 0.25985 0.03052 ASaccharom 45 0.40495 0.04126 23 iterations until convergence AGiardia 46 0.74815 0.06719 log L: -35966.83 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): (((beta_Macet:0.66341,(beta_Enter:0.35781,(beta_Therm:0.33220,(beta_Cyani:0.44440, (beta_Sacch:0.25615,(beta_aquif:0.56410,(beta_Arabi:0.24846,Beta_human:0.19277) :0.11395):0.00602):0.13463):0.07190):0.05904):0.47335):1.47507,(BNanoarcha:1.10083, (BSulfolo:0.49283,(BPyrobacul:0.72444,(B_Mjanna:0.30219,((B_halobact:0.45339, BMacetiv:0.32013):0.17468,(BGiardia:0.90412,((BCryptospo:0.18052, BPlasmodiu:0.21997):0.08453,((Bhomo:0.25809,(BEncephali:0.30632, BSaccharom:0.22234):0.09214):0.03659,((B_cyanidiu:0.23165,BTrypanoso:0.39553) :0.05477,(BArabidops:0.04778,BOryza:0.02982):0.19015):0.05637):0.11585) :0.35264):0.28474):0.05506):0.12327):0.09527):0.37432):2.24050):0.00001, ((AEnterococ:0.44162,((AGiardia:0.74815,(ASaccharom:0.40495,(ACyanidium:0.23691, (AArabidops:0.30340,A1Homo1_Ho:0.25985):0.02873):0.08319):0.17949) :0.49267,((APyrobacul:0.64845,ASulfolobu:0.42982):0.36319,(AjMethanoc:0.27372, (AHalobacte:0.42489,A_Maceti:0.38205):0.22892):0.05385):0.02413):0.13311) :3.48152,(alpha_acet:0.72060,(alphaGeoba:0.30147,((alpha_Sacc:0.54777, alphaChlor:0.28009):0.15091,(alphaAquif:0.37804,(alphaEnter:0.43585, alpha_Ther:0.32298):0.05263):0.03479):0.01858):0.57819):2.93817):0.00001, (F_Borrelia:0.81674,(F_Styphi:1.06720,(F_Bsubtili:0.52497,F_Treponem:0.69823) :0.18126):0.37301):1.56984); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---23 alpha_acet :--------70 : : :-21 alphaGeoba : :--69 : : :--22 alpha_Sacc : : :-65 : : : :-19 alphaChlor : :-68 : : :--17 alphaAquif : :-67 : : :--20 alphaEnter : :-66 : :--18 alpha_Ther :--86 : : :----16 BNanoarcha : :------85 : : :--11 BSulfolo : :-84 : : :---10 BPyrobacul : :-83 : : :-14 B_Mjanna : :-82 : : :--12 B_halobact : : :-71 : : : :--13 BMacetiv : :-81 : : :---15 BGiardia : :-80 : : :-8 BCryptospo : : :-72 : : : :-9 BPlasmodiu : :--79 : : :-7 Bhomo : : :-74 : : : : :-6 BEncephali : : : :-73 : : : :-5 BSaccharom : :-78 : : :-3 B_cyanidiu : : :-75 : : : :--4 BTrypanoso : :-77 : : :-1 BArabidops : :-76 : :-2 BOryza : : :---27 F_Borrelia :-----89 : : :----26 F_Styphi : :--88 : : :--25 F_Bsubtili : :-87 : :---24 F_Treponem : : :---35 beta_Macet : :----53 : : : :--32 beta_Enter : : :--52 : : : :--31 beta_Therm : : :-51 : : : :--34 beta_Cyani : : :-50 : : : :-30 beta_Sacch : : :-49 : : : :--33 beta_aquif : : :-48 : : : :-28 beta_Arabi : : :-47 : : :-29 Beta_human :--64 : :--41 AEnterococ :-----------63 : :---46 AGiardia : :--57 : : : :--45 ASaccharom : : :-56 : : : :-43 ACyanidium : : :-55 : : : :-42 AArabidops : : :-54 : : :-44 A1Homo1_Ho :-62 : :---36 APyrobacul : :--58 : : :--37 ASulfolobu :-61 : :-40 AjMethanoc :-60 : :--39 AHalobacte :-59 :--38 A_Maceti branch length S.E. branch length S.E. BArabidops 1 0.04773 0.01379 47 0.11401 0.02774 BOryza 2 0.02978 0.01187 48 0.00596 0.01186 B_cyanidiu 3 0.23116 0.03303 49 0.13447 0.03143 BTrypanoso 4 0.39491 0.04359 50 0.07174 0.02587 BSaccharom 5 0.22200 0.03280 51 0.05641 0.03180 BEncephali 6 0.30576 0.03830 52 0.45558 0.08378 Bhomo 7 0.25781 0.03332 53 1.17114 0.19647 BCryptospo 8 0.18014 0.02860 54 0.02882 0.01703 BPlasmodiu 9 0.21967 0.03105 55 0.08289 0.02684 BPyrobacul 10 0.72398 0.07348 56 0.17960 0.04028 BSulfolo 11 0.48658 0.06292 57 0.49285 0.05779 B_halobact 12 0.45247 0.05426 58 0.36131 0.05053 BMacetiv 13 0.31977 0.04621 59 0.22852 0.03764 B_Mjanna 14 0.30025 0.04494 60 0.05452 0.02487 BGiardia 15 0.90175 0.08677 61 0.02261 0.02578 BNanoarcha 16 1.19758 0.13164 62 0.11519 0.04955 alphaAquif 17 0.37766 0.04297 63 3.24584 0.35938 alpha_Ther 18 0.32245 0.04153 64 0.38823 0.17511 alphaChlor 19 0.27989 0.03905 65 0.15085 0.03339 alphaEnter 20 0.43525 0.04703 66 0.05222 0.02123 alphaGeoba 21 0.30160 0.03898 67 0.03457 0.02072 alpha_Sacc 22 0.54637 0.05529 68 0.01828 0.02091 alpha_acet 23 0.68811 0.09701 69 0.61017 0.09653 F_Treponem 24 0.69751 0.08395 70 2.34966 0.30946 F_Bsubtili 25 0.52257 0.07597 71 0.17404 0.03897 F_Styphi 26 1.06292 0.11322 72 0.08423 0.02628 F_Borrelia 27 0.80902 0.11245 73 0.09192 0.02499 beta_Arabi 28 0.24803 0.03188 74 0.03654 0.01714 Beta_human 29 0.19243 0.02863 75 0.05464 0.02125 beta_Sacch 30 0.25555 0.03476 76 0.18992 0.02978 beta_Therm 31 0.33218 0.04289 77 0.05624 0.02041 beta_Enter 32 0.35941 0.04625 78 0.11593 0.02742 beta_aquif 33 0.56257 0.05643 79 0.35228 0.05552 beta_Cyani 34 0.44356 0.04863 80 0.28373 0.05264 beta_Macet 35 0.67878 0.08836 81 0.05639 0.02967 APyrobacul 36 0.64673 0.06270 82 0.12226 0.03801 ASulfolobu 37 0.42976 0.05093 83 0.09988 0.04436 A_Maceti 38 0.38151 0.04341 84 0.27406 0.09558 AHalobacte 39 0.42442 0.04623 85 1.78699 0.26573 AjMethanoc 40 0.27353 0.03619 86 0.61719 0.19527 AEnterococ 41 0.45999 0.05355 87 0.18286 0.06944 AArabidops 42 0.30294 0.03272 88 0.37856 0.09953 ACyanidium 43 0.23641 0.02967 89 1.37174 0.21378 A1Homo1_Ho 44 0.25960 0.03048 ASaccharom 45 0.40460 0.04121 23 iterations until convergence AGiardia 46 0.74627 0.06702 log L: -35955.99 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (((beta_Macet:0.67878,(beta_Enter:0.35941,(beta_Therm:0.33218,(beta_Cyani:0.44356, (beta_Sacch:0.25555,(beta_aquif:0.56257,(beta_Arabi:0.24803,Beta_human:0.19243) :0.11401):0.00596):0.13447):0.07174):0.05641):0.45558):1.17114,(AEnterococ:0.45999, ((AGiardia:0.74627,(ASaccharom:0.40460,(ACyanidium:0.23641,(AArabidops:0.30294, A1Homo1_Ho:0.25960):0.02882):0.08289):0.17960):0.49285,((APyrobacul:0.64673, ASulfolobu:0.42976):0.36131,(AjMethanoc:0.27353,(AHalobacte:0.42442, A_Maceti:0.38151):0.22852):0.05452):0.02261):0.11519):3.24584):0.38823, ((alpha_acet:0.68811,(alphaGeoba:0.30160,((alpha_Sacc:0.54637,alphaChlor:0.27989) :0.15085,(alphaAquif:0.37766,(alphaEnter:0.43525,alpha_Ther:0.32245) :0.05222):0.03457):0.01828):0.61017):2.34966,(BNanoarcha:1.19758,( BSulfolo:0.48658,(BPyrobacul:0.72398,(B_Mjanna:0.30025,((B_halobact:0.45247, BMacetiv:0.31977):0.17404,(BGiardia:0.90175,((BCryptospo:0.18014, BPlasmodiu:0.21967):0.08423,((Bhomo:0.25781,(BEncephali:0.30576, BSaccharom:0.22200):0.09192):0.03654,((B_cyanidiu:0.23116,BTrypanoso:0.39491) :0.05464,(BArabidops:0.04773,BOryza:0.02978):0.18992):0.05624):0.11593) :0.35228):0.28373):0.05639):0.12226):0.09988):0.27406):1.78699):0.61719, (F_Borrelia:0.80902,(F_Styphi:1.06292,(F_Bsubtili:0.52257,F_Treponem:0.69751) :0.18286):0.37856):1.37174); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--41 AEnterococ :-----------63 : : :---46 AGiardia : : :--57 : : : : :--45 ASaccharom : : : :-56 : : : : :-43 ACyanidium : : : :-55 : : : : :-42 AArabidops : : : :-54 : : : :-44 A1Homo1_Ho : :-62 : : :---36 APyrobacul : : :--58 : : : :--37 ASulfolobu : :-61 : : :-40 AjMethanoc : :-60 : : :--39 AHalobacte : :-59 : :--38 A_Maceti : : :---27 F_Borrelia : :----66 : : : :----26 F_Styphi : : :--65 : : : :--25 F_Bsubtili : : :-64 : : :---24 F_Treponem : :--73 : : : :---23 alpha_acet : : :---------72 : : : :-21 alphaGeoba : : :--71 : : : :--22 alpha_Sacc : : : :-67 : : : : :-19 alphaChlor : : :-70 : : : :--17 alphaAquif : : :-69 : : : :--20 alphaEnter : : :-68 : : :--18 alpha_Ther :--89 : : :----16 BNanoarcha : :-------88 : : :--11 BSulfolo : :--87 : : :---10 BPyrobacul : :-86 : : :-14 B_Mjanna : :-85 : : :--12 B_halobact : : :-74 : : : :--13 BMacetiv : :-84 : : :---15 BGiardia : :-83 : : :-8 BCryptospo : : :-75 : : : :-9 BPlasmodiu : :--82 : : :-7 Bhomo : : :-77 : : : : :-6 BEncephali : : : :-76 : : : :-5 BSaccharom : :-81 : : :-3 B_cyanidiu : : :-78 : : : :--4 BTrypanoso : :-80 : : :-1 BArabidops : :-79 : :-2 BOryza : : :---35 beta_Macet :----53 : :--32 beta_Enter :--52 : :--31 beta_Therm :-51 : :--34 beta_Cyani :-50 : :-30 beta_Sacch :-49 : :--33 beta_aquif :-48 : :-28 beta_Arabi :-47 :-29 Beta_human branch length S.E. branch length S.E. BArabidops 1 0.04788 0.01383 47 0.11419 0.02780 BOryza 2 0.02988 0.01190 48 0.00597 0.01159 B_cyanidiu 3 0.23207 0.03316 49 0.13500 0.03155 BTrypanoso 4 0.39633 0.04376 50 0.07247 0.02597 BSaccharom 5 0.22278 0.03293 51 0.05823 0.03197 BEncephali 6 0.30700 0.03846 52 0.45726 0.08402 Bhomo 7 0.25859 0.03344 53 1.20466 0.19935 BCryptospo 8 0.18083 0.02871 54 0.02889 0.01699 BPlasmodiu 9 0.22047 0.03117 55 0.08321 0.02691 BPyrobacul 10 0.72574 0.07371 56 0.18002 0.04041 BSulfolo 11 0.49562 0.06354 57 0.49497 0.05804 B_halobact 12 0.45460 0.05451 58 0.36297 0.05075 BMacetiv 13 0.32082 0.04639 59 0.22948 0.03777 B_Mjanna 14 0.30284 0.04524 60 0.05465 0.02492 BGiardia 15 0.90631 0.08724 61 0.02267 0.02568 BNanoarcha 16 1.10291 0.13064 62 0.11893 0.04971 alphaAquif 17 0.37877 0.04312 63 3.26279 0.36078 alpha_Ther 18 0.32363 0.04169 64 0.17986 0.06939 alphaChlor 19 0.28087 0.03921 65 0.37117 0.09928 alphaEnter 20 0.43667 0.04720 66 1.22467 0.21116 alphaGeoba 21 0.30202 0.03908 67 0.15088 0.03348 alpha_Sacc 22 0.54859 0.05554 68 0.05258 0.02130 alpha_acet 23 0.69133 0.09731 69 0.03516 0.02090 F_Treponem 24 0.70015 0.08437 70 0.01844 0.02092 F_Bsubtili 25 0.52541 0.07635 71 0.61203 0.09682 F_Styphi 26 1.07447 0.11430 72 2.64154 0.32526 F_Borrelia 27 0.82212 0.11312 73 0.39083 0.15494 beta_Arabi 28 0.24889 0.03199 74 0.17511 0.03916 Beta_human 29 0.19303 0.02873 75 0.08459 0.02639 beta_Sacch 30 0.25639 0.03488 76 0.09234 0.02508 beta_Therm 31 0.33276 0.04300 77 0.03663 0.01720 beta_Enter 32 0.35892 0.04635 78 0.05490 0.02134 beta_aquif 33 0.56521 0.05671 79 0.19053 0.02989 beta_Cyani 34 0.44530 0.04884 80 0.05648 0.02049 beta_Macet 35 0.68174 0.08869 81 0.11617 0.02752 APyrobacul 36 0.64909 0.06295 82 0.35367 0.05578 ASulfolobu 37 0.43072 0.05110 83 0.28542 0.05292 A_Maceti 38 0.38262 0.04355 84 0.05500 0.02965 AHalobacte 39 0.42594 0.04640 85 0.12349 0.03825 AjMethanoc 40 0.27416 0.03629 86 0.09399 0.04452 AEnterococ 41 0.45817 0.05371 87 0.37830 0.10468 AArabidops 42 0.30376 0.03281 88 2.13972 0.27930 ACyanidium 43 0.23708 0.02976 89 0.32675 0.16831 A1Homo1_Ho 44 0.26031 0.03056 ASaccharom 45 0.40584 0.04134 24 iterations until convergence AGiardia 46 0.74889 0.06728 log L: -35957.80 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): ((beta_Macet:0.68174,(beta_Enter:0.35892,(beta_Therm:0.33276,(beta_Cyani:0.44530, (beta_Sacch:0.25639,(beta_aquif:0.56521,(beta_Arabi:0.24889,Beta_human:0.19303) :0.11419):0.00597):0.13500):0.07247):0.05823):0.45726):1.20466,(AEnterococ:0.45817, ((AGiardia:0.74889,(ASaccharom:0.40584,(ACyanidium:0.23708,(AArabidops:0.30376, A1Homo1_Ho:0.26031):0.02889):0.08321):0.18002):0.49497,((APyrobacul:0.64909, ASulfolobu:0.43072):0.36297,(AjMethanoc:0.27416,(AHalobacte:0.42594, A_Maceti:0.38262):0.22948):0.05465):0.02267):0.11893):3.26279,((( F_Borrelia:0.82212,(F_Styphi:1.07447,(F_Bsubtili:0.52541,F_Treponem:0.70015) :0.17986):0.37117):1.22467,(alpha_acet:0.69133,(alphaGeoba:0.30202, ((alpha_Sacc:0.54859,alphaChlor:0.28087):0.15088,(alphaAquif:0.37877, (alphaEnter:0.43667,alpha_Ther:0.32363):0.05258):0.03516):0.01844) :0.61203):2.64154):0.39083,(BNanoarcha:1.10291,(BSulfolo:0.49562, (BPyrobacul:0.72574,(B_Mjanna:0.30284,((B_halobact:0.45460,BMacetiv:0.32082) :0.17511,(BGiardia:0.90631,((BCryptospo:0.18083,BPlasmodiu:0.22047) :0.08459,((Bhomo:0.25859,(BEncephali:0.30700,BSaccharom:0.22278) :0.09234):0.03663,((B_cyanidiu:0.23207,BTrypanoso:0.39633):0.05490, (BArabidops:0.04788,BOryza:0.02988):0.19053):0.05648):0.11617):0.35367) :0.28542):0.05500):0.12349):0.09399):0.37830):2.13972):0.32675); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--41 AEnterococ :-----------67 : : :---46 AGiardia : : :--61 : : : : :--45 ASaccharom : : : :-60 : : : : :-43 ACyanidium : : : :-59 : : : : :-42 AArabidops : : : :-58 : : : :-44 A1Homo1_Ho : :-66 : : :---36 APyrobacul : : :--62 : : : :--37 ASulfolobu : :-65 : : :-40 AjMethanoc : :-64 : : :--39 AHalobacte : :-63 : :--38 A_Maceti : : :---23 alpha_acet : :--------73 : : : :-21 alphaGeoba : : :--72 : : : :--22 alpha_Sacc : : : :-68 : : : : :-19 alphaChlor : : :-71 : : : :--17 alphaAquif : : :-70 : : : :--20 alphaEnter : : :-69 : : :--18 alpha_Ther :--89 : : :----16 BNanoarcha : :------88 : : :--11 BSulfolo : :-87 : : :---10 BPyrobacul : :-86 : : :-14 B_Mjanna : :-85 : : :--12 B_halobact : : :-74 : : : :--13 BMacetiv : :-84 : : :---15 BGiardia : :-83 : : :-8 BCryptospo : : :-75 : : : :-9 BPlasmodiu : :--82 : : :-7 Bhomo : : :-77 : : : : :-6 BEncephali : : : :-76 : : : :-5 BSaccharom : :-81 : : :-3 B_cyanidiu : : :-78 : : : :--4 BTrypanoso : :-80 : : :-1 BArabidops : :-79 : :-2 BOryza : : :---35 beta_Macet : :-----53 : : : :--32 beta_Enter : : :--52 : : : :--31 beta_Therm : : :-51 : : : :--34 beta_Cyani : : :-50 : : : :-30 beta_Sacch : : :-49 : : : :--33 beta_aquif : : :-48 : : : :-28 beta_Arabi : : :-47 : : :-29 Beta_human :-57 : :---27 F_Borrelia :-----56 : :----26 F_Styphi :--55 : :--25 F_Bsubtili :-54 :---24 F_Treponem branch length S.E. branch length S.E. BArabidops 1 0.04774 0.01379 47 0.11388 0.02774 BOryza 2 0.02977 0.01187 48 0.00599 0.01190 B_cyanidiu 3 0.23120 0.03304 49 0.13454 0.03144 BTrypanoso 4 0.39502 0.04360 50 0.07143 0.02588 BSaccharom 5 0.22200 0.03280 51 0.05852 0.03195 BEncephali 6 0.30582 0.03830 52 0.46967 0.08407 Bhomo 7 0.25784 0.03332 53 1.37195 0.20290 BCryptospo 8 0.18023 0.02861 54 0.18414 0.06962 BPlasmodiu 9 0.21963 0.03105 55 0.37414 0.09925 BPyrobacul 10 0.72322 0.07345 56 1.46988 0.21623 BSulfolo 11 0.48540 0.06291 57 0.15737 0.14121 B_halobact 12 0.45247 0.05427 58 0.02873 0.01699 BMacetiv 13 0.31981 0.04622 59 0.08300 0.02686 B_Mjanna 14 0.30072 0.04499 60 0.17948 0.04028 BGiardia 15 0.90179 0.08679 61 0.49216 0.05777 BNanoarcha 16 1.17454 0.13100 62 0.36207 0.05059 alphaAquif 17 0.37778 0.04298 63 0.22856 0.03763 alpha_Ther 18 0.32255 0.04153 64 0.05398 0.02481 alphaChlor 19 0.27994 0.03907 65 0.02377 0.02573 alphaEnter 20 0.43534 0.04704 66 0.13104 0.04980 alphaGeoba 21 0.30186 0.03900 67 3.31178 0.37022 alpha_Sacc 22 0.54663 0.05531 68 0.15093 0.03341 alpha_acet 23 0.69088 0.09714 69 0.05226 0.02125 F_Treponem 24 0.69804 0.08397 70 0.03445 0.02069 F_Bsubtili 25 0.52275 0.07597 71 0.01823 0.02082 F_Styphi 26 1.06082 0.11306 72 0.60673 0.09655 F_Borrelia 27 0.81356 0.11256 73 2.41957 0.31367 beta_Arabi 28 0.24808 0.03189 74 0.17429 0.03899 Beta_human 29 0.19256 0.02865 75 0.08455 0.02631 beta_Sacch 30 0.25573 0.03478 76 0.09196 0.02499 beta_Therm 31 0.33231 0.04290 77 0.03657 0.01715 beta_Enter 32 0.35773 0.04622 78 0.05468 0.02126 beta_aquif 33 0.56299 0.05646 79 0.18991 0.02979 beta_Cyani 34 0.44357 0.04863 80 0.05623 0.02041 beta_Macet 35 0.66543 0.08808 81 0.11568 0.02742 APyrobacul 36 0.64725 0.06275 82 0.35224 0.05553 ASulfolobu 37 0.42972 0.05095 83 0.28384 0.05265 A_Maceti 38 0.38170 0.04342 84 0.05605 0.02967 AHalobacte 39 0.42432 0.04624 85 0.12282 0.03808 AjMethanoc 40 0.27350 0.03619 86 0.10123 0.04438 AEnterococ 41 0.44326 0.05341 87 0.29693 0.09701 AArabidops 42 0.30313 0.03274 88 1.71600 0.25845 ACyanidium 43 0.23664 0.02969 89 0.58565 0.19630 A1Homo1_Ho 44 0.25958 0.03049 ASaccharom 45 0.40450 0.04121 22 iterations until convergence AGiardia 46 0.74703 0.06708 log L: -35958.65 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (((beta_Macet:0.66543,(beta_Enter:0.35773,(beta_Therm:0.33231,(beta_Cyani:0.44357, (beta_Sacch:0.25573,(beta_aquif:0.56299,(beta_Arabi:0.24808,Beta_human:0.19256) :0.11388):0.00599):0.13454):0.07143):0.05852):0.46967):1.37195,(F_Borrelia:0.81356, (F_Styphi:1.06082,(F_Bsubtili:0.52275,F_Treponem:0.69804):0.18414) :0.37414):1.46988):0.15737,(AEnterococ:0.44326,((AGiardia:0.74703, (ASaccharom:0.40450,(ACyanidium:0.23664,(AArabidops:0.30313,A1Homo1_Ho:0.25958) :0.02873):0.08300):0.17948):0.49216,((APyrobacul:0.64725,ASulfolobu:0.42972) :0.36207,(AjMethanoc:0.27350,(AHalobacte:0.42432,A_Maceti:0.38170) :0.22856):0.05398):0.02377):0.13104):3.31178,((alpha_acet:0.69088, (alphaGeoba:0.30186,((alpha_Sacc:0.54663,alphaChlor:0.27994):0.15093, (alphaAquif:0.37778,(alphaEnter:0.43534,alpha_Ther:0.32255):0.05226) :0.03445):0.01823):0.60673):2.41957,(BNanoarcha:1.17454,(BSulfolo:0.48540, (BPyrobacul:0.72322,(B_Mjanna:0.30072,((B_halobact:0.45247,BMacetiv:0.31981) :0.17429,(BGiardia:0.90179,((BCryptospo:0.18023,BPlasmodiu:0.21963) :0.08455,((Bhomo:0.25784,(BEncephali:0.30582,BSaccharom:0.22200) :0.09196):0.03657,((B_cyanidiu:0.23120,BTrypanoso:0.39502):0.05468, (BArabidops:0.04774,BOryza:0.02977):0.18991):0.05623):0.11568):0.35224) :0.28384):0.05605):0.12282):0.10123):0.29693):1.71600):0.58565); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 5 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---27 F_Borrelia :-----67 : : :----26 F_Styphi : :--66 : : :--25 F_Bsubtili : :-65 : :---24 F_Treponem : : :---23 alpha_acet : :--------73 : : : :-21 alphaGeoba : : :--72 : : : :--22 alpha_Sacc : : : :-68 : : : : :-19 alphaChlor : : :-71 : : : :--17 alphaAquif : : :-70 : : : :--20 alphaEnter : : :-69 : : :--18 alpha_Ther :---89 : : :-----16 BNanoarcha : : :-76 : : : : :-14 B_Mjanna : : : :-75 : : : : :--12 B_halobact : : : :-74 : : : :--13 BMacetiv : : :-78 : : : : :--11 BSulfolo : : : :-77 : : : :---10 BPyrobacul : :-------88 : : :---15 BGiardia : :-87 : : :-8 BCryptospo : : :-79 : : : :-9 BPlasmodiu : :--86 : : :-7 Bhomo : : :-81 : : : : :-6 BEncephali : : : :-80 : : : :-5 BSaccharom : :-85 : : :-3 B_cyanidiu : : :-82 : : : :--4 BTrypanoso : :-84 : : :-1 BArabidops : :-83 : :-2 BOryza : : :---35 beta_Macet : :----53 : : : :--32 beta_Enter : : :--52 : : : :--31 beta_Therm : : :-51 : : : :--34 beta_Cyani : : :-50 : : : :-30 beta_Sacch : : :-49 : : : :--33 beta_aquif : : :-48 : : : :-28 beta_Arabi : : :-47 : : :-29 Beta_human :--64 : :--41 AEnterococ :-----------63 : :---46 AGiardia : :--57 : : : :--45 ASaccharom : : :-56 : : : :-43 ACyanidium : : :-55 : : : :-42 AArabidops : : :-54 : : :-44 A1Homo1_Ho :-62 : :---36 APyrobacul : :--58 : : :--37 ASulfolobu :-61 : :-40 AjMethanoc :-60 : :--39 AHalobacte :-59 :--38 A_Maceti branch length S.E. branch length S.E. BArabidops 1 0.04742 0.01375 47 0.11395 0.02770 BOryza 2 0.02993 0.01187 48 0.00602 0.01175 B_cyanidiu 3 0.23112 0.03300 49 0.13373 0.03132 BTrypanoso 4 0.39386 0.04349 50 0.07163 0.02582 BSaccharom 5 0.22158 0.03274 51 0.05532 0.03169 BEncephali 6 0.30497 0.03821 52 0.44220 0.08324 Bhomo 7 0.25770 0.03330 53 1.19419 0.19982 BCryptospo 8 0.17944 0.02852 54 0.02880 0.01701 BPlasmodiu 9 0.21946 0.03102 55 0.08287 0.02680 BPyrobacul 10 0.72319 0.07296 56 0.17979 0.04022 BSulfolo 11 0.56558 0.06375 57 0.49205 0.05767 B_halobact 12 0.46013 0.05475 58 0.36038 0.05041 BMacetiv 13 0.31353 0.04566 59 0.22807 0.03757 B_Mjanna 14 0.28607 0.04371 60 0.05549 0.02485 BGiardia 15 0.89696 0.08687 61 0.02145 0.02583 BNanoarcha 16 1.54268 0.13661 62 0.10908 0.04923 alphaAquif 17 0.37668 0.04287 63 3.20706 0.35592 alpha_Ther 18 0.32162 0.04143 64 0.43224 0.18203 alphaChlor 19 0.27999 0.03902 65 0.18436 0.06951 alphaEnter 20 0.43433 0.04692 66 0.38841 0.09953 alphaGeoba 21 0.30062 0.03889 67 1.32378 0.21196 alpha_Sacc 22 0.54519 0.05515 68 0.15037 0.03333 alpha_acet 23 0.75298 0.09744 69 0.05260 0.02122 F_Treponem 24 0.69608 0.08378 70 0.03445 0.02061 F_Bsubtili 25 0.51965 0.07574 71 0.01886 0.02091 F_Styphi 26 1.06058 0.11310 72 0.54167 0.09468 F_Borrelia 27 0.79721 0.11189 73 2.24822 0.30131 beta_Arabi 28 0.24756 0.03181 74 0.19391 0.03985 Beta_human 29 0.19212 0.02858 75 0.08012 0.03227 beta_Sacch 30 0.25504 0.03470 76 0.03298 0.02349 beta_Therm 31 0.33149 0.04280 77 0.07136 0.03520 beta_Enter 32 0.35998 0.04622 78 0.08242 0.04242 beta_aquif 33 0.56102 0.05627 79 0.07080 0.02529 beta_Cyani 34 0.44309 0.04856 80 0.09153 0.02496 beta_Macet 35 0.69029 0.08847 81 0.03626 0.01712 APyrobacul 36 0.64540 0.06254 82 0.05365 0.02111 ASulfolobu 37 0.42901 0.05083 83 0.19016 0.02980 A_Maceti 38 0.38119 0.04336 84 0.05688 0.02048 AHalobacte 39 0.42397 0.04617 85 0.12903 0.02828 AjMethanoc 40 0.27320 0.03614 86 0.36174 0.05635 AEnterococ 41 0.46600 0.05352 87 0.18455 0.05000 AArabidops 42 0.30253 0.03268 88 2.04818 0.27625 ACyanidium 43 0.23608 0.02963 89 0.65851 0.20081 A1Homo1_Ho 44 0.25939 0.03045 ASaccharom 45 0.40394 0.04114 23 iterations until convergence AGiardia 46 0.74471 0.06689 log L: -35961.07 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (((beta_Macet:0.69029,(beta_Enter:0.35998,(beta_Therm:0.33149,(beta_Cyani:0.44309, (beta_Sacch:0.25504,(beta_aquif:0.56102,(beta_Arabi:0.24756,Beta_human:0.19212) :0.11395):0.00602):0.13373):0.07163):0.05532):0.44220):1.19419,(AEnterococ:0.46600, ((AGiardia:0.74471,(ASaccharom:0.40394,(ACyanidium:0.23608,(AArabidops:0.30253, A1Homo1_Ho:0.25939):0.02880):0.08287):0.17979):0.49205,((APyrobacul:0.64540, ASulfolobu:0.42901):0.36038,(AjMethanoc:0.27320,(AHalobacte:0.42397, A_Maceti:0.38119):0.22807):0.05549):0.02145):0.10908):3.20706):0.43224, (F_Borrelia:0.79721,(F_Styphi:1.06058,(F_Bsubtili:0.51965,F_Treponem:0.69608) :0.18436):0.38841):1.32378,((alpha_acet:0.75298,(alphaGeoba:0.30062, ((alpha_Sacc:0.54519,alphaChlor:0.27999):0.15037,(alphaAquif:0.37668, (alphaEnter:0.43433,alpha_Ther:0.32162):0.05260):0.03445):0.01886) :0.54167):2.24822,(((BNanoarcha:1.54268,(B_Mjanna:0.28607,(B_halobact:0.46013, BMacetiv:0.31353):0.19391):0.08012):0.03298,(BSulfolo:0.56558,BPyrobacul:0.72319) :0.07136):0.08242,(BGiardia:0.89696,((BCryptospo:0.17944,BPlasmodiu:0.21946) :0.07080,((Bhomo:0.25770,(BEncephali:0.30497,BSaccharom:0.22158) :0.09153):0.03626,((B_cyanidiu:0.23112,BTrypanoso:0.39386):0.05365, (BArabidops:0.04742,BOryza:0.02993):0.19016):0.05688):0.12903):0.36174) :0.18455):2.04818):0.65851); COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH ------------------------------------------------------------------------------- 1 -35966.83 10.85 5.9476 0.0340 - 0.2260 + 0.0017 - + 2 -35955.99 0.00 <---- best 1.0000 + 1.0000 + 0.2837 + best 3 -35957.80 1.82 6.5436 0.3980 + 0.6930 + 0.2858 + + 4 -35958.65 2.66 3.7974 0.2360 + 0.6750 + 0.1619 + + 5 -35961.07 5.08 10.4562 0.3090 + 0.4570 + 0.2668 + + The columns show the results and p-values of the following tests: 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa 2000, Goldman et al., 2001, Kishino-Hasegawa 1989) SH - Shimodaira-Hasegawa test (2000) ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002) 2sKH - two sided Kishino-Hasegawa test (1989) Plus signs denote the confidence sets. Minus signs denote significant exclusion. All tests used 5% significance level. 1sKH, SH, and ELW performed 1000 resamplings using the RELL method. 1sKH and 2sKH are correct to the 2nd position after the the decimal point of the log-likelihoods. TIME STAMP Date and time: Mon Mar 24 17:38:39 2008 Runtime (excl. input) : 4119 seconds (= 68.7 minutes = 1.1 hours) Runtime (incl. input) : 9812 seconds (= 163.5 minutes = 2.7 hours)