PUZZLE 4.0 Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 41 sequences with 649 amino acid sites Number of constant sites: 7 (= 1.1% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 9.6% pi(R) = 5.3% pi(N) = 4.1% pi(D) = 5.6% pi(C) = 1.1% pi(Q) = 2.5% pi(E) = 6.9% pi(G) = 8.4% pi(H) = 2.0% pi(I) = 7.1% pi(L) = 8.8% pi(K) = 5.8% pi(M) = 2.8% pi(F) = 3.4% pi(P) = 4.6% pi(S) = 5.5% pi(T) = 5.1% pi(W) = 0.5% pi(Y) = 2.8% pi(V) = 7.9% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value cMethanoba passed 22.17% [594] Archaeoglo failed 1.30% [350] cMethanoco failed 0.02% [448] *Schizosac passed 99.61% [575] *Saccharom passed 84.71% [625] Deinococcu passed 82.45% [919] Pseudomona passed 8.63% [312] Agrobacter passed 65.85% [324] Arabidopsi passed 100.00% [355] Synechocys failed 3.94% [286] Clostridiu passed 56.56% [312] Aquifex failed 2.36% [301] Ecoli2 passed 66.86% [249] Haemophilu passed 90.93% [278] Leptospira passed 56.57% [259] Thermotoga passed 66.55% [273] Bacteroide passed 69.53% [365] Lactococcu passed 87.28% [255] *Ecoli failed 1.70% [214] Sphingomon failed 0.86% [273] *Bacillus6 passed 22.98% [280] *Agrobacte passed 22.97% [310] Mycobacter passed 6.39% [193] Corynebact passed 14.64% [179] Sulfolobus passed 23.13% [311] cSchizosac passed 78.00% [292] cKluyverom passed 73.16% [412] cHomosapie passed 34.33% [386] cCelegans2 passed 96.64% [416] cMusmuscul failed 4.69% [300] cHomosapi_ passed 8.79% [315] cCelegans passed 38.22% [457] cArabidops passed 44.73% [354] cNicotiana passed 68.45% [368] cKluyvero_ passed 31.27% [306] cBostaurus passed 72.34% [178] cCelegans3 passed 94.06% [183] cNicotian_ passed 57.38% [251] cThermus passed 33.51% [306] Pyrococcus failed 0.31% [692] cCaldococc failed 2.96% [584] The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. The number in square brackets indicates how often each sequence is involved in one of the 3660 completely unresolved quartets of the quartet puzzling tree search. 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. 41 cMethanoba 0.00000 0.70953 0.81513 1.07279 0.99951 1.04313 1.22283 1.38206 1.22226 1.28900 1.26664 1.13302 1.24920 1.24716 1.21330 1.13440 1.39366 1.07651 1.35569 1.37712 1.41235 1.22481 1.33773 1.19940 1.06379 1.23301 1.15094 1.30697 1.33231 1.25425 1.25278 1.27735 1.28367 1.27233 1.19589 1.22493 1.25559 1.06402 0.97905 1.14484 1.37605 Archaeoglo 0.70953 0.00000 0.88299 1.03996 0.98259 1.09501 1.14010 1.25269 1.27601 1.28332 1.19981 1.12017 1.21362 1.23992 1.16019 1.09992 1.50388 1.26462 1.34356 1.34066 1.38350 1.26278 1.24574 1.12200 0.89686 1.29754 1.14506 1.25846 1.22573 1.34842 1.34059 1.31209 1.12236 1.16904 1.19414 1.02409 1.12872 0.99306 1.07775 1.22607 1.57267 cMethanoco 0.81513 0.88299 0.00000 1.01881 1.13298 1.07427 1.28956 1.43895 1.50104 1.49151 1.31952 1.16174 1.36998 1.32298 1.29849 1.17529 1.30655 1.22331 1.41618 1.49244 1.43867 1.52777 1.39944 1.23586 0.97335 1.44882 1.53082 1.73875 1.62223 1.73321 1.74159 1.50083 1.55750 1.49013 1.27316 1.40944 1.49824 1.30705 1.19537 1.09146 1.46366 *Schizosac 1.07279 1.03996 1.01881 0.00000 0.49827 1.18633 1.38655 1.49289 1.54191 1.52062 1.36223 1.28341 1.60012 1.56073 1.61082 1.50468 1.64991 1.27670 1.48630 1.49196 1.58004 1.37438 1.56107 1.56915 1.19545 1.34962 1.36843 1.53948 1.54757 1.55628 1.56872 1.61835 1.42871 1.40929 1.36873 1.31279 1.37793 1.28557 1.36689 1.22552 1.68477 *Saccharom 0.99951 0.98259 1.13298 0.49827 0.00000 1.35167 1.34380 1.51578 1.51329 1.47747 1.39021 1.22514 1.53611 1.49231 1.53654 1.42803 1.58699 1.31858 1.36588 1.38716 1.48846 1.33752 1.49635 1.54763 1.12702 1.38832 1.35546 1.62326 1.56505 1.48448 1.50198 1.69180 1.48993 1.52149 1.46906 1.40053 1.41794 1.42751 1.57360 1.19547 1.70743 Deinococcu 1.04313 1.09501 1.07427 1.18633 1.35167 0.00000 1.55556 1.77732 1.61699 1.52099 1.41108 1.49418 1.52621 1.63899 1.66539 1.44292 1.57258 1.48616 1.58451 1.52291 1.53211 1.50032 1.76226 1.62364 1.16999 1.54215 1.53545 1.57252 1.48863 1.52057 1.55355 1.41595 1.48081 1.45096 1.56104 1.57152 1.63990 1.60375 1.47911 1.37989 1.63896 Pseudomona 1.22283 1.14010 1.28956 1.38655 1.34380 1.55556 0.00000 0.63088 0.64115 0.60799 0.71328 0.68610 0.75639 0.73574 0.71719 0.84070 0.99790 0.80926 1.50422 1.56672 1.54705 1.57384 1.29808 1.15259 1.37822 1.80386 1.56615 1.72612 1.73785 1.82694 1.81710 1.75322 1.67597 1.72961 1.77954 1.76998 1.70405 1.69912 1.45463 1.42009 1.99468 Agrobacter 1.38206 1.25269 1.43895 1.49289 1.51578 1.77732 0.63088 0.00000 0.90433 0.86065 0.94998 0.91307 0.92545 0.95605 0.91525 0.92609 1.31574 1.04480 1.61757 1.72629 1.63488 1.66093 1.55018 1.45046 1.51239 1.89690 1.72632 1.93732 1.73920 1.90029 1.85268 1.86385 1.69535 1.73010 1.89597 1.66374 1.72675 1.75542 1.68376 1.47613 2.15625 Arabidopsi 1.22226 1.27601 1.50104 1.54191 1.51329 1.61699 0.64115 0.90433 0.00000 0.46416 0.67618 0.71649 0.89054 0.85700 0.83227 0.90448 1.10501 0.93005 1.54773 1.46738 1.44969 1.65749 1.45853 1.26281 1.35868 1.90376 1.75817 1.80789 1.85590 1.97295 2.01290 1.78617 1.90474 1.94534 1.83295 1.82421 1.78039 1.74825 1.64968 1.58274 2.42159 Synechocys 1.28900 1.28332 1.49151 1.52062 1.47747 1.52099 0.60799 0.86065 0.46416 0.00000 0.70113 0.69087 0.85651 0.80896 0.79034 0.89844 1.10963 0.94138 1.48251 1.41759 1.54415 1.65287 1.41032 1.38517 1.47042 1.87042 1.64120 1.69015 1.77410 1.85954 1.87799 1.64138 1.65142 1.69269 1.70236 1.70533 1.65459 1.68320 1.62396 1.54410 2.09842 Clostridiu 1.26664 1.19981 1.31952 1.36223 1.39021 1.41108 0.71328 0.94998 0.67618 0.70113 0.00000 0.61152 0.74944 0.69251 0.76612 0.65639 0.89646 0.88007 1.59212 1.55680 1.49283 1.54281 1.32900 1.14182 1.29194 1.80328 1.62442 1.92679 1.68140 1.83503 1.81406 1.67144 1.83328 1.84448 1.79957 1.78398 1.78237 1.70210 1.55549 1.46817 1.75989 Aquifex 1.13302 1.12017 1.16174 1.28341 1.22514 1.49418 0.68610 0.91307 0.71649 0.69087 0.61152 0.00000 0.87308 0.72275 0.73767 0.71126 0.91322 0.80255 1.40576 1.54719 1.43816 1.46718 1.26926 1.14515 1.27107 1.64108 1.61649 1.73073 1.68509 1.83887 1.82780 1.69155 1.76835 1.81689 1.58321 1.67126 1.66235 1.48568 1.49300 1.36968 1.80245 Ecoli2 1.24920 1.21362 1.36998 1.60012 1.53611 1.52621 0.75639 0.92545 0.89054 0.85651 0.74944 0.87308 0.00000 0.38328 0.60781 0.68284 1.02710 0.92910 1.44238 1.44974 1.50193 1.48021 1.27804 1.14421 1.44312 1.84960 1.59289 1.80167 1.81425 1.87616 1.85584 1.70599 1.73805 1.79936 1.64569 1.58565 1.61353 1.57883 1.55046 1.48089 1.88060 Haemophilu 1.24716 1.23992 1.32298 1.56073 1.49231 1.63899 0.73574 0.95605 0.85700 0.80896 0.69251 0.72275 0.38328 0.00000 0.54026 0.72004 1.00274 0.95612 1.35543 1.38143 1.56131 1.48799 1.52982 1.23209 1.48982 1.81834 1.71575 1.81027 1.78984 1.86182 1.84731 1.66158 1.62277 1.70577 1.71624 1.73063 1.80449 1.57081 1.62436 1.33421 1.79311 Leptospira 1.21330 1.16019 1.29849 1.61082 1.53654 1.66539 0.71719 0.91525 0.83227 0.79034 0.76612 0.73767 0.60781 0.54026 0.00000 0.74922 1.12493 0.88334 1.60724 1.49302 1.65373 1.65472 1.52376 1.37446 1.48602 1.84019 1.75749 1.82399 1.84891 1.93193 1.92555 1.72142 1.75826 1.81094 1.73615 1.64538 1.88641 1.61243 1.55725 1.42869 1.95576 Thermotoga 1.13440 1.09992 1.17529 1.50468 1.42803 1.44292 0.84070 0.92609 0.90448 0.89844 0.65639 0.71126 0.68284 0.72004 0.74922 0.00000 0.99244 0.86774 1.42065 1.44937 1.42234 1.31992 1.32637 1.16950 1.30339 1.71235 1.45187 1.81318 1.63419 1.80294 1.81475 1.63555 1.66052 1.68063 1.59277 1.59066 1.61341 1.48915 1.36703 1.48832 1.86648 Bacteroide 1.39366 1.50388 1.30655 1.64991 1.58699 1.57258 0.99790 1.31574 1.10501 1.10963 0.89646 0.91322 1.02710 1.00274 1.12493 0.99244 0.00000 0.87877 1.73368 1.83271 1.73316 1.70261 1.42960 1.34266 1.56643 2.06125 1.86070 1.94280 1.77177 1.91187 1.91876 1.88758 2.04366 1.91940 1.81022 1.98095 1.89252 1.90028 1.79883 1.45151 1.86252 Lactococcu 1.07651 1.26462 1.22331 1.27670 1.31858 1.48616 0.80926 1.04480 0.93005 0.94138 0.88007 0.80255 0.92910 0.95612 0.88334 0.86774 0.87877 0.00000 1.38893 1.48836 1.55817 1.26468 1.32208 1.15138 1.41472 1.51533 1.57530 1.63709 1.67810 1.74308 1.72210 1.67365 1.64965 1.65589 1.56611 1.54159 1.55937 1.47870 1.41374 1.23224 1.81038 *Ecoli 1.35569 1.34356 1.41618 1.48630 1.36588 1.58451 1.50422 1.61757 1.54773 1.48251 1.59212 1.40576 1.44238 1.35543 1.60724 1.42065 1.73368 1.38893 0.00000 0.59442 0.76210 0.81484 1.16898 1.08146 1.59909 1.86940 1.70928 1.88023 1.79102 1.86917 1.90778 1.95111 1.84050 1.86318 1.73754 1.69411 1.74721 1.72886 1.70001 1.40380 2.32360 Sphingomon 1.37712 1.34066 1.49244 1.49196 1.38716 1.52291 1.56672 1.72629 1.46738 1.41759 1.55680 1.54719 1.44974 1.38143 1.49302 1.44937 1.83271 1.48836 0.59442 0.00000 0.65918 0.86129 1.11378 1.08929 1.71421 1.62823 1.63915 1.75668 1.74921 1.87714 1.86800 1.88670 1.76222 1.84540 1.52608 1.68321 1.62762 1.64378 1.56221 1.45775 2.14802 *Bacillus6 1.41235 1.38350 1.43867 1.58004 1.48846 1.53211 1.54705 1.63488 1.44969 1.54415 1.49283 1.43816 1.50193 1.56131 1.65373 1.42234 1.73316 1.55817 0.76210 0.65918 0.00000 0.94567 1.13567 1.09055 1.65099 1.90989 1.75342 2.01513 1.91269 2.15044 2.18244 1.84134 1.95632 1.98737 1.69116 1.84849 1.78310 1.94499 1.66151 1.62206 2.06672 *Agrobacte 1.22481 1.26278 1.52777 1.37438 1.33752 1.50032 1.57384 1.66093 1.65749 1.65287 1.54281 1.46718 1.48021 1.48799 1.65472 1.31992 1.70261 1.26468 0.81484 0.86129 0.94567 0.00000 1.16007 1.02871 1.50069 1.65431 1.52680 1.75226 1.79184 1.76229 1.77097 1.64415 1.67919 1.68640 1.53763 1.60202 1.66925 1.59826 1.58209 1.37777 2.14050 Mycobacter 1.33773 1.24574 1.39944 1.56107 1.49635 1.76226 1.29808 1.55018 1.45853 1.41032 1.32900 1.26926 1.27804 1.52982 1.52376 1.32637 1.42960 1.32208 1.16898 1.11378 1.13567 1.16007 0.00000 0.39253 1.60681 1.85046 1.69170 1.88267 1.73551 2.01627 1.99311 1.89752 1.77224 1.84134 1.63179 1.66563 1.62019 1.61057 1.64751 1.52125 1.89440 Corynebact 1.19940 1.12200 1.23586 1.56915 1.54763 1.62364 1.15259 1.45046 1.26281 1.38517 1.14182 1.14515 1.14421 1.23209 1.37446 1.16950 1.34266 1.15138 1.08146 1.08929 1.09055 1.02871 0.39253 0.00000 1.49886 1.64041 1.50268 1.73879 1.58095 1.76386 1.76457 1.65826 1.60638 1.60144 1.45616 1.53265 1.60588 1.44518 1.49843 1.36056 1.73347 Sulfolobus 1.06379 0.89686 0.97335 1.19545 1.12702 1.16999 1.37822 1.51239 1.35868 1.47042 1.29194 1.27107 1.44312 1.48982 1.48602 1.30339 1.56643 1.41472 1.59909 1.71421 1.65099 1.50069 1.60681 1.49886 0.00000 1.21439 1.22817 1.38444 1.35196 1.27419 1.27390 1.47700 1.24710 1.31632 1.23581 1.08876 1.25954 1.12604 1.22043 1.37270 1.59877 cSchizosac 1.23301 1.29754 1.44882 1.34962 1.38832 1.54215 1.80386 1.89690 1.90376 1.87042 1.80328 1.64108 1.84960 1.81834 1.84019 1.71235 2.06125 1.51533 1.86940 1.62823 1.90989 1.65431 1.85046 1.64041 1.21439 0.00000 0.49226 0.91629 0.94772 0.89310 0.88561 0.91544 0.83644 0.87810 1.05745 0.92539 1.01279 0.89452 1.22265 1.41600 1.64820 cKluyverom 1.15094 1.14506 1.53082 1.36843 1.35546 1.53545 1.56615 1.72632 1.75817 1.64120 1.62442 1.61649 1.59289 1.71575 1.75749 1.45187 1.86070 1.57530 1.70928 1.63915 1.75342 1.52680 1.69170 1.50268 1.22817 0.49226 0.00000 0.93404 0.92902 0.89291 0.89363 0.90028 0.86352 0.86951 0.96985 1.04098 0.99460 0.94380 1.14335 1.43120 1.67757 cHomosapie 1.30697 1.25846 1.73875 1.53948 1.62326 1.57252 1.72612 1.93732 1.80789 1.69015 1.92679 1.73073 1.80167 1.81027 1.82399 1.81318 1.94280 1.63709 1.88023 1.75668 2.01513 1.75226 1.88267 1.73879 1.38444 0.91629 0.93404 0.00000 0.61264 0.95460 0.94417 1.04284 0.97951 0.96748 1.27932 1.08437 1.14529 0.97908 1.42324 1.64595 1.86028 cCelegans2 1.33231 1.22573 1.62223 1.54757 1.56505 1.48863 1.73785 1.73920 1.85590 1.77410 1.68140 1.68509 1.81425 1.78984 1.84891 1.63419 1.77177 1.67810 1.79102 1.74921 1.91269 1.79184 1.73551 1.58095 1.35196 0.94772 0.92902 0.61264 0.00000 0.95634 0.97681 1.08656 0.99661 0.94133 1.23145 1.26494 1.20508 1.09273 1.40074 1.61885 1.86756 cMusmuscul 1.25425 1.34842 1.73321 1.55628 1.48448 1.52057 1.82694 1.90029 1.97295 1.85954 1.83503 1.83887 1.87616 1.86182 1.93193 1.80294 1.91187 1.74308 1.86917 1.87714 2.15044 1.76229 2.01627 1.76386 1.27419 0.89310 0.89291 0.95460 0.95634 0.00000 0.04792 0.73270 0.99947 0.97204 1.19824 1.08765 1.15706 1.03121 1.35032 1.54477 1.90104 cHomosapi_ 1.25278 1.34059 1.74159 1.56872 1.50198 1.55355 1.81710 1.85268 2.01290 1.87799 1.81406 1.82780 1.85584 1.84731 1.92555 1.81475 1.91876 1.72210 1.90778 1.86800 2.18244 1.77097 1.99311 1.76457 1.27390 0.88561 0.89363 0.94417 0.97681 0.04792 0.00000 0.73724 1.00175 0.97371 1.22144 1.08271 1.14438 1.02797 1.34918 1.52181 1.89902 cCelegans 1.27735 1.31209 1.50083 1.61835 1.69180 1.41595 1.75322 1.86385 1.78617 1.64138 1.67144 1.69155 1.70599 1.66158 1.72142 1.63555 1.88758 1.67365 1.95111 1.88670 1.84134 1.64415 1.89752 1.65826 1.47700 0.91544 0.90028 1.04284 1.08656 0.73270 0.73724 0.00000 1.02478 1.00593 1.24889 1.21703 1.21630 1.14421 1.15848 1.66010 1.84107 cArabidops 1.28367 1.12236 1.55750 1.42871 1.48993 1.48081 1.67597 1.69535 1.90474 1.65142 1.83328 1.76835 1.73805 1.62277 1.75826 1.66052 2.04366 1.64965 1.84050 1.76222 1.95632 1.67919 1.77224 1.60638 1.24710 0.83644 0.86352 0.97951 0.99661 0.99947 1.00175 1.02478 0.00000 0.28658 1.17229 1.00894 1.05030 0.94269 1.23931 1.60171 1.72255 cNicotiana 1.27233 1.16904 1.49013 1.40929 1.52149 1.45096 1.72961 1.73010 1.94534 1.69269 1.84448 1.81689 1.79936 1.70577 1.81094 1.68063 1.91940 1.65589 1.86318 1.84540 1.98737 1.68640 1.84134 1.60144 1.31632 0.87810 0.86951 0.96748 0.94133 0.97204 0.97371 1.00593 0.28658 0.00000 1.05506 1.00093 1.02062 0.87933 1.11417 1.56942 1.67233 cKluyvero_ 1.19589 1.19414 1.27316 1.36873 1.46906 1.56104 1.77954 1.89597 1.83295 1.70236 1.79957 1.58321 1.64569 1.71624 1.73615 1.59277 1.81022 1.56611 1.73754 1.52608 1.69116 1.53763 1.63179 1.45616 1.23581 1.05745 0.96985 1.27932 1.23145 1.19824 1.22144 1.24889 1.17229 1.05506 0.00000 0.73753 0.70210 0.84092 1.06288 1.50000 1.62521 cBostaurus 1.22493 1.02409 1.40944 1.31279 1.40053 1.57152 1.76998 1.66374 1.82421 1.70533 1.78398 1.67126 1.58565 1.73063 1.64538 1.59066 1.98095 1.54159 1.69411 1.68321 1.84849 1.60202 1.66563 1.53265 1.08876 0.92539 1.04098 1.08437 1.26494 1.08765 1.08271 1.21703 1.00894 1.00093 0.73753 0.00000 0.42452 0.70721 1.13023 1.48185 1.70179 cCelegans3 1.25559 1.12872 1.49824 1.37793 1.41794 1.63990 1.70405 1.72675 1.78039 1.65459 1.78237 1.66235 1.61353 1.80449 1.88641 1.61341 1.89252 1.55937 1.74721 1.62762 1.78310 1.66925 1.62019 1.60588 1.25954 1.01279 0.99460 1.14529 1.20508 1.15706 1.14438 1.21630 1.05030 1.02062 0.70210 0.42452 0.00000 0.69394 1.17139 1.58350 1.59294 cNicotian_ 1.06402 0.99306 1.30705 1.28557 1.42751 1.60375 1.69912 1.75542 1.74825 1.68320 1.70210 1.48568 1.57883 1.57081 1.61243 1.48915 1.90028 1.47870 1.72886 1.64378 1.94499 1.59826 1.61057 1.44518 1.12604 0.89452 0.94380 0.97908 1.09273 1.03121 1.02797 1.14421 0.94269 0.87933 0.84092 0.70721 0.69394 0.00000 1.07799 1.34176 1.45407 cThermus 0.97905 1.07775 1.19537 1.36689 1.57360 1.47911 1.45463 1.68376 1.64968 1.62396 1.55549 1.49300 1.55046 1.62436 1.55725 1.36703 1.79883 1.41374 1.70001 1.56221 1.66151 1.58209 1.64751 1.49843 1.22043 1.22265 1.14335 1.42324 1.40074 1.35032 1.34918 1.15848 1.23931 1.11417 1.06288 1.13023 1.17139 1.07799 0.00000 1.75035 1.48490 Pyrococcus 1.14484 1.22607 1.09146 1.22552 1.19547 1.37989 1.42009 1.47613 1.58274 1.54410 1.46817 1.36968 1.48089 1.33421 1.42869 1.48832 1.45151 1.23224 1.40380 1.45775 1.62206 1.37777 1.52125 1.36056 1.37270 1.41600 1.43120 1.64595 1.61885 1.54477 1.52181 1.66010 1.60171 1.56942 1.50000 1.48185 1.58350 1.34176 1.75035 0.00000 1.91607 cCaldococc 1.37605 1.57267 1.46366 1.68477 1.70743 1.63896 1.99468 2.15625 2.42159 2.09842 1.75989 1.80245 1.88060 1.79311 1.95576 1.86648 1.86252 1.81038 2.32360 2.14802 2.06672 2.14050 1.89440 1.73347 1.59877 1.64820 1.67757 1.86028 1.86756 1.90104 1.89902 1.84107 1.72255 1.67233 1.62521 1.70179 1.59294 1.45407 1.48490 1.91607 0.00000 Average distance (over all possible pairs of sequences): 1.42052 TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 10000 Analysed quartets: 101270 Unresolved quartets: 3660 (= 3.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Bacteroide :-------------90: : :---Lactococcu : : :---Clostridiu : :---------69: :-98: : :---Aquifex : : : : : : :---Ecoli2 : : : :-70: : : : :-57: :---Haemophilu : : : : : : :-62:-63: :-------Leptospira : : : : : :-----------Thermotoga : : : : :---Pseudomona :-86: : :-83: : : : : :---Agrobacter : : :-----56: : : : :---Arabidopsi : : :-80: : : :---Synechocys : : : : :---Mycobacter : : :--------100: : : : :---Corynebact : : : : :-----97: :---*Ecoli : : :-94: : : :-99: :---Sphingomon : : : : : :-98: :-------*Bacillus6 : : : :-----------*Agrobacte : : :---*Schizosac :---------------------82: : :---*Saccharom : : :---cThermus : :-----------------91: : : :---cCaldococc : : : : :---cArabidops : : :---------97: :-53: : : :---cNicotiana : : : : : : : : :---cSchizosac : :-82: :---------94: : : : :-95: :---cKluyverom : : : : : : : : : : :---cHomosapie : : : : : :-----92: : : : : : : :---cCelegans2 : : : : :-52: : : : : : :---cMusmuscul : : : : : :-86: : : :-85: :-71: :---cHomosapi_ : : : : : : : :-------cCelegans : : : : : : :---cBostaurus : : : :-78: : : : :-59: :---cCelegans3 : : : : : : : :-----90: :-------cKluyvero_ : : : : : :-----------cNicotian_ : : : :---------------------------cMethanoco : : : :---------------------------Deinococcu : : : :---------------------------Sulfolobus : : : :---------------------------Pyrococcus : :-------------------------------Archaeoglo : :-------------------------------cMethanoba Quartet puzzling tree (in CLUSTAL W notation): (cMethanoba,((((Bacteroide,Lactococcu)90,((Clostridiu,Aquifex)69, (((Ecoli2,Haemophilu)70,Leptospira)57,Thermotoga)63,((Pseudomona, Agrobacter)83,(Arabidopsi,Synechocys)80)56)62)98,((Mycobacter, Corynebact)100,(((*Ecoli,Sphingomon)94,*Bacillus6)99,*Agrobacte)98)97)86, (*Schizosac,*Saccharom)82,((cThermus,cCaldococc)91,(((cArabidops, cNicotiana)97,(cSchizosac,cKluyverom)94,((cHomosapie,cCelegans2)92, ((cMusmuscul,cHomosapi_)86,cCelegans)71)52)95,(((cBostaurus, cCelegans3)78,cKluyvero_)59,cNicotian_)90)85)82,cMethanoco, Deinococcu,Sulfolobus,Pyrococcus)53,Archaeoglo); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 10000 puzzling steps: Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ********** ********** **..****** ********** * : 9990 ********** ********.. .********* ********** * : 9892 ********** ********.. ..******** ********** * : 9787 ******.... ........** ********** ********** * : 9771 ********** ********.. ....****** ********** * : 9717 ********** ********** ********** **..****** * : 9651 ********** ********** *****..... ....****** * : 9470 ********** ********.. ********** ********** * : 9386 ********** ********** *****..*** ********** * : 9358 ********** ********** *******..* ********** * : 9196 ********** ********** ********** ********.* . : 9087 ********** ******..** ********** ********** * : 9005 ********** ********** ********** ****....** * : 8956 ******.... .......... ....****** ********** * : 8649 ********** ********** *********. .********* * : 8592 ********** ********** *****..... ........** * : 8489 ******..** ********** ********** ********** * : 8339 ***..***** ********** ********** ********** * : 8219 ********** ********** *****..... .........* . : 8203 ********.. ********** ********** ********** * : 7971 ********** ********** ********** *****..*** * : 7751 ********** ********** *********. ..******** * : 7147 ********** **..****** ********** ********** * : 7009 ********** ..******** ********** ********** * : 6911 ********** **....**** ********** ********** * : 6263 ******.... ......**** ********** ********** * : 6226 ********** ********** ********** ****...*** * : 5888 ********** **...***** ********** ********** * : 5740 ******.... ********** ********** ********** * : 5624 **........ .......... .......... .......... . : 5301 ********** ********** *******... ..******** * : 5211 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **.**.**** ********** ********** ********** * : 4111 ********** ********** ********** *****...** * : 3843 ******.... ..******** ********** ********** * : 3683 ********** ********** *****..... ..******** * : 3605 ***..***** ********** ********** *********. * : 3366 ********** ********** ****...... .........* . : 3293 ********** **..*.**** ********** ********** * : 3217 ********** **.**.**** ********** ********** * : 2911 ********** ********** *****..*** **..****** * : 2670 ********** ********** *******... ....****** * : 2401 ********.. ..******** ********** ********** * : 2241 ********** ********** *****..**. ..******** * : 2111 ********** ********** ********** ******..** * : 1964 *.*....... .......... .......... .......... . : 1924 **.**.**** ********** ****.***** ********** * : 1821 **.******* ********** ********** *********. * : 1796 *.*..*.... .......... .......... .......... . : 1687 ********** ********** *******..* **..****** * : 1680 ********** ..****..** ********** ********** * : 1607 ********** ********** *******... .********* * : 1464 (1520 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-------17 Bacteroide :--42 : :----18 Lactococcu :---51 : : :----11 Clostridiu : : :-43 : : : :----12 Aquifex : :--50 : : :---13 Ecoli2 : : :--44 : : : :--14 Haemophilu : : :--45 : : : :----15 Leptospira : :--46 : : :-----16 Thermotoga : : : : :--7 Pseudomona : : :--47 : : : :------8 Agrobacter : :--49 : : :---9 Arabidopsi : :---48 : :---10 Synechocys :----57 : : :----23 Mycobacter : : :----52 : : : :--24 Corynebact : :----56 : : :----19 *Ecoli : : :-53 : : : :----20 Sphingomon : : :--54 : : : :-----21 *Bacillus6 : :---55 : :-----22 *Agrobacte : : :---4 *Schizosac :------58 : :----5 *Saccharom : : :------39 cThermus : :--59 : : :-----------41 cCaldococc :----71 : : :--33 cArabidops : : :-----60 : : : :--34 cNicotiana : : :--66 : : : : :---26 cSchizosac : : : :---61 : : : : :---27 cKluyverom : : : : : : : : :----28 cHomosapie : : : : :---62 : : : : : :----29 cCelegans2 : : : :--65 : : : : :-30 cMusmuscul : : : : :----63 : : : : : :-31 cHomosapi_ : : : :---64 : : : :-----32 cCelegans : :---70 : : :---36 cBostaurus : : :--67 : : : :---37 cCelegans3 : : :--68 : : : :-----35 cKluyvero_ : :--69 : :----38 cNicotian_ :--72 : :-------3 cMethanoco : : : :---------6 Deinococcu : : : :--------25 Sulfolobus : : : :----------40 Pyrococcus : :----2 Archaeoglo : :----1 cMethanoba branch length S.E. branch length S.E. cMethanoba 1 0.34063 0.04431 42 0.11409 0.03377 Archaeoglo 2 0.35989 0.04585 43 0.07568 0.02496 cMethanoco 3 0.56831 0.05749 44 0.14238 0.02934 *Schizosac 4 0.24092 0.03783 45 0.13914 0.02997 *Saccharom 5 0.27442 0.03976 46 0.09974 0.02621 Deinococcu 6 0.72917 0.08077 47 0.15863 0.03206 Pseudomona 7 0.16666 0.03096 48 0.18762 0.03319 Agrobacter 8 0.47856 0.04906 49 0.12760 0.02993 Arabidopsi 9 0.27108 0.03659 50 0.13977 0.03396 Synechocys 10 0.21309 0.03221 51 0.26553 0.04848 Clostridiu 11 0.33492 0.03994 52 0.35921 0.05178 Aquifex 12 0.29375 0.03762 53 0.07954 0.02850 Ecoli2 13 0.22234 0.03193 54 0.14669 0.03560 Haemophilu 14 0.17071 0.02846 55 0.23793 0.04533 Leptospira 15 0.29595 0.03780 56 0.27723 0.05012 Thermotoga 16 0.36933 0.04344 57 0.30212 0.04936 Bacteroide 17 0.54785 0.05752 58 0.50512 0.05753 Lactococcu 18 0.35724 0.04592 59 0.10326 0.03983 *Ecoli 19 0.28668 0.03963 60 0.44069 0.04914 Sphingomon 20 0.31899 0.04133 61 0.24709 0.03846 *Bacillus6 21 0.42631 0.05164 62 0.25686 0.04061 *Agrobacte 22 0.38647 0.04798 63 0.33142 0.04296 Mycobacter 23 0.28212 0.03741 64 0.20667 0.03969 Corynebact 24 0.11379 0.02861 65 0.09166 0.02805 Sulfolobus 25 0.68296 0.06590 66 0.17688 0.03496 cSchizosac 26 0.27217 0.03733 67 0.17931 0.03366 cKluyverom 27 0.23785 0.03556 68 0.11954 0.03278 cHomosapie 28 0.31244 0.04037 69 0.09211 0.03164 cCelegans2 29 0.31231 0.04053 70 0.18741 0.03917 cMusmuscul 30 0.00979 0.00870 71 0.35962 0.05152 cHomosapi_ 31 0.03830 0.01083 72 0.17527 0.03516 cCelegans 32 0.44226 0.04855 cArabidops 33 0.13966 0.02756 cNicotiana 34 0.15684 0.02816 cKluyvero_ 35 0.40898 0.04633 cBostaurus 36 0.22060 0.03352 cCelegans3 37 0.22570 0.03380 cNicotian_ 38 0.34588 0.04214 cThermus 39 0.52820 0.06023 Pyrococcus 40 0.83623 0.07992 13 iterations until convergence cCaldococc 41 0.96318 0.08663 log L: -25884.67 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (cMethanoba:0.34063,((((Bacteroide:0.54785,Lactococcu:0.35724)90:0.11409, ((Clostridiu:0.33492,Aquifex:0.29375)69:0.07568,(((Ecoli2:0.22234, Haemophilu:0.17071)70:0.14238,Leptospira:0.29595)57:0.13914,Thermotoga:0.36933) 63:0.09974,((Pseudomona:0.16666,Agrobacter:0.47856)83:0.15863,(Arabidopsi:0.27108, Synechocys:0.21309)80:0.18762)56:0.12760)62:0.13977)98:0.26553,( (Mycobacter:0.28212,Corynebact:0.11379)100:0.35921,(((*Ecoli:0.28668, Sphingomon:0.31899)94:0.07954,*Bacillus6:0.42631)99:0.14669,*Agrobacte:0.38647) 98:0.23793)97:0.27723)86:0.30212,(*Schizosac:0.24092,*Saccharom:0.27442) 82:0.50512,((cThermus:0.52820,cCaldococc:0.96318)91:0.10326,(((cArabidops:0.13966, cNicotiana:0.15684)97:0.44069,(cSchizosac:0.27217,cKluyverom:0.23785) 94:0.24709,((cHomosapie:0.31244,cCelegans2:0.31231)92:0.25686,(( cMusmuscul:0.00979,cHomosapi_:0.03830)86:0.33142,cCelegans:0.44226) 71:0.20667)52:0.09166)95:0.17688,(((cBostaurus:0.22060,cCelegans3:0.22570) 78:0.17931,cKluyvero_:0.40898)59:0.11954,cNicotian_:0.34588)90:0.09211) 85:0.18741)82:0.35962,cMethanoco:0.56831,Deinococcu:0.72917,Sulfolobus:0.68296, Pyrococcus:0.83623)53:0.17527,Archaeoglo:0.35989); TIME STAMP Date and time: Fri Dec 3 03:09:00 1999 Runtime: 9159 seconds (= 152.7 minutes = 2.5 hours)