PUZZLE 4.0 Type of analysis: likelihood mapping 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: 34 sequences with 688 amino acid sites Number of constant sites: 98 (= 14.2% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 7.4% pi(R) = 5.2% pi(N) = 3.0% pi(D) = 5.9% pi(C) = 0.9% pi(Q) = 3.4% pi(E) = 7.7% pi(G) = 8.3% pi(H) = 1.1% pi(I) = 6.0% pi(L) = 8.3% pi(K) = 5.4% pi(M) = 3.1% pi(F) = 3.5% pi(P) = 5.1% pi(S) = 6.8% pi(T) = 5.7% pi(W) = 1.1% pi(Y) = 3.9% pi(V) = 8.1% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value Daucus passed 99.32% Gossypium passed 95.90% Mung_bean passed 99.54% Beta_vul passed 99.03% Brassica passed 97.97% Hordeum passed 99.55% AAcetabula passed 99.99% BAcetabula passed 99.97% Cyanidium passed 99.72% Mus passed 99.91% Homo1 passed 99.95% Homo2 passed 99.95% Bos passed 99.99% Sus passed 100.00% A1Gallus passed 100.00% A2Gallus passed 99.86% Manduca passed 99.97% Drosophila passed 99.80% Saccharom passed 96.82% Candida passed 98.53% Schizosac passed 84.95% Neurospora passed 80.75% Entamoeba passed 99.36% Plasmodium passed 45.97% Trypanosom passed 98.11% Giardia passed 7.72% Sulfolobus passed 22.61% BMethanosa passed 99.51% MMethanosa passed 89.69% jMethanoco passed 9.29% Haloferax failed 0.07% Halobact failed 0.03% Enterococc failed 4.70% Thermus passed 8.49% 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. 34 Daucus 0.00000 0.04518 0.05022 0.06632 0.03017 0.09954 0.31374 0.30562 0.37177 0.43174 0.43188 0.44093 0.43452 0.42830 0.43608 0.50546 0.43105 0.45852 0.57508 0.61079 0.58718 0.57503 0.49653 0.57674 0.48325 0.80743 0.96143 0.88016 0.88740 0.83552 0.92238 0.96109 0.93653 0.83162 Gossypium 0.04518 0.00000 0.05227 0.07045 0.05812 0.10791 0.30281 0.31403 0.37248 0.41730 0.41539 0.42196 0.41327 0.41173 0.41431 0.48162 0.42539 0.44695 0.57530 0.60787 0.58479 0.57409 0.50963 0.56288 0.46590 0.79544 0.97465 0.87610 0.88328 0.84043 0.92141 0.96693 0.95415 0.84506 Mung_bean 0.05022 0.05227 0.00000 0.07910 0.05952 0.11136 0.31500 0.31261 0.36440 0.41883 0.41744 0.42168 0.41990 0.41373 0.42374 0.49194 0.42029 0.45410 0.57137 0.60155 0.58332 0.57625 0.50656 0.57882 0.47704 0.82323 0.98082 0.88134 0.87873 0.83557 0.93433 0.97713 0.93675 0.84231 Beta_vul 0.06632 0.07045 0.07910 0.00000 0.07836 0.12622 0.30387 0.31158 0.36930 0.42422 0.42287 0.42912 0.42066 0.41911 0.42391 0.48815 0.42416 0.45257 0.58046 0.59439 0.58599 0.58921 0.51965 0.58085 0.46222 0.80866 0.97126 0.90073 0.90399 0.84841 0.95424 0.95737 0.94491 0.85364 Brassica 0.03017 0.05812 0.05952 0.07836 0.00000 0.10217 0.31259 0.30734 0.36297 0.42922 0.42936 0.43596 0.43025 0.42403 0.43199 0.50115 0.43170 0.45704 0.56206 0.60253 0.58920 0.57876 0.50103 0.57628 0.48159 0.82072 0.96858 0.88577 0.88634 0.83936 0.92866 0.97092 0.94571 0.83118 Hordeum 0.09954 0.10791 0.11136 0.12622 0.10217 0.00000 0.31787 0.31090 0.34059 0.41464 0.41757 0.41645 0.40887 0.40703 0.40941 0.47990 0.40093 0.43064 0.52715 0.56100 0.50473 0.53652 0.48614 0.56988 0.46296 0.79937 1.00285 0.89388 0.90547 0.83883 0.91371 0.95960 0.95428 0.85625 AAcetabula 0.31374 0.30281 0.31500 0.30387 0.31259 0.31787 0.00000 0.04906 0.36832 0.41449 0.41684 0.40324 0.41306 0.40885 0.42716 0.49612 0.39762 0.42906 0.53816 0.54460 0.51832 0.54465 0.46938 0.54345 0.44558 0.78785 0.97744 0.88931 0.87804 0.82074 0.89821 0.91055 0.92224 0.85115 BAcetabula 0.30562 0.31403 0.31261 0.31158 0.30734 0.31090 0.04906 0.00000 0.38022 0.44558 0.44324 0.43888 0.44184 0.43956 0.45372 0.52566 0.41792 0.44196 0.54614 0.55412 0.54130 0.56410 0.49731 0.56763 0.47674 0.81395 0.99128 0.92719 0.90509 0.84737 0.91679 0.93824 0.93128 0.87557 Cyanidium 0.37177 0.37248 0.36440 0.36930 0.36297 0.34059 0.36832 0.38022 0.00000 0.37740 0.39039 0.40640 0.37606 0.37558 0.39151 0.46099 0.41235 0.43673 0.53174 0.52465 0.52668 0.51132 0.46482 0.55614 0.46360 0.74670 0.91518 0.79463 0.82175 0.78339 0.88216 0.88949 0.85984 0.78463 Mus 0.43174 0.41730 0.41883 0.42422 0.42922 0.41464 0.41449 0.44558 0.37740 0.00000 0.03278 0.18579 0.01952 0.02614 0.05477 0.09615 0.19728 0.21162 0.49788 0.49743 0.47629 0.52162 0.48025 0.59844 0.50096 0.84795 1.00298 0.88763 0.89248 0.82688 0.90157 0.93772 0.93266 0.89078 Homo1 0.43188 0.41539 0.41744 0.42287 0.42936 0.41757 0.41684 0.44324 0.39039 0.03278 0.00000 0.18379 0.01956 0.02944 0.05485 0.09630 0.20369 0.21481 0.48828 0.49181 0.47343 0.51965 0.47711 0.61166 0.49353 0.84970 1.00338 0.89364 0.90407 0.84035 0.90341 0.94919 0.93455 0.89147 Homo2 0.44093 0.42196 0.42168 0.42912 0.43596 0.41645 0.40324 0.43888 0.40640 0.18579 0.18379 0.00000 0.17367 0.18491 0.18614 0.24128 0.10796 0.14767 0.46108 0.45539 0.47657 0.50289 0.45704 0.58963 0.51111 0.82282 0.95749 0.87546 0.89243 0.82242 0.90931 0.92685 0.90947 0.87490 Bos 0.43452 0.41327 0.41990 0.42066 0.43025 0.40887 0.41306 0.44184 0.37606 0.01952 0.01956 0.17367 0.00000 0.01623 0.04127 0.08151 0.19182 0.20363 0.49460 0.48633 0.46657 0.51203 0.46957 0.59809 0.48675 0.84123 0.99433 0.87690 0.88924 0.82439 0.89182 0.93543 0.91747 0.87641 Sus 0.42830 0.41173 0.41373 0.41911 0.42403 0.40703 0.40885 0.43956 0.37558 0.02614 0.02944 0.18491 0.01623 0.00000 0.04803 0.08888 0.20169 0.20646 0.50416 0.49601 0.47814 0.52582 0.47807 0.59989 0.49218 0.84850 1.00043 0.88919 0.89519 0.83487 0.90049 0.94431 0.92002 0.87967 A1Gallus 0.43608 0.41431 0.42374 0.42391 0.43199 0.40941 0.42716 0.45372 0.39151 0.05477 0.05485 0.18614 0.04127 0.04803 0.00000 0.03647 0.21021 0.21354 0.50566 0.49939 0.47456 0.52783 0.48556 0.60025 0.48281 0.83917 0.98423 0.88403 0.89657 0.83647 0.90418 0.94624 0.91706 0.87566 A2Gallus 0.50546 0.48162 0.49194 0.48815 0.50115 0.47990 0.49612 0.52566 0.46099 0.09615 0.09630 0.24128 0.08151 0.08888 0.03647 0.00000 0.26505 0.26896 0.59221 0.58070 0.56138 0.60823 0.56794 0.68445 0.55976 0.92849 1.08710 0.97950 0.98667 0.91380 0.98743 1.04379 0.97941 0.97273 Manduca 0.43105 0.42539 0.42029 0.42416 0.43170 0.40093 0.39762 0.41792 0.41235 0.19728 0.20369 0.10796 0.19182 0.20169 0.21021 0.26505 0.00000 0.15096 0.47734 0.46309 0.49815 0.50390 0.45903 0.56945 0.52011 0.81052 0.97457 0.85356 0.86137 0.82148 0.90215 0.91814 0.89540 0.87668 Drosophila 0.45852 0.44695 0.45410 0.45257 0.45704 0.43064 0.42906 0.44196 0.43673 0.21162 0.21481 0.14767 0.20363 0.20646 0.21354 0.26896 0.15096 0.00000 0.51661 0.50726 0.50856 0.54200 0.46017 0.59019 0.52553 0.83661 0.98202 0.88082 0.90140 0.84273 0.91530 0.96722 0.90745 0.91149 Saccharom 0.57508 0.57530 0.57137 0.58046 0.56206 0.52715 0.53816 0.54614 0.53174 0.49788 0.48828 0.46108 0.49460 0.50416 0.50566 0.59221 0.47734 0.51661 0.00000 0.13668 0.44714 0.33617 0.56064 0.69706 0.61684 0.85448 0.96891 0.90989 0.92923 0.87082 1.00256 1.00671 0.96299 0.86239 Candida 0.61079 0.60787 0.60155 0.59439 0.60253 0.56100 0.54460 0.55412 0.52465 0.49743 0.49181 0.45539 0.48633 0.49601 0.49939 0.58070 0.46309 0.50726 0.13668 0.00000 0.42881 0.33363 0.54287 0.68761 0.60873 0.86834 0.97921 0.89529 0.90546 0.84611 0.98637 0.98960 0.96413 0.85822 Schizosac 0.58718 0.58479 0.58332 0.58599 0.58920 0.50473 0.51832 0.54130 0.52668 0.47629 0.47343 0.47657 0.46657 0.47814 0.47456 0.56138 0.49815 0.50856 0.44714 0.42881 0.00000 0.45982 0.54915 0.66459 0.56376 0.85892 1.07433 0.94976 0.97260 0.91881 1.00828 1.00784 1.06313 0.86941 Neurospora 0.57503 0.57409 0.57625 0.58921 0.57876 0.53652 0.54465 0.56410 0.51132 0.52162 0.51965 0.50289 0.51203 0.52582 0.52783 0.60823 0.50390 0.54200 0.33617 0.33363 0.45982 0.00000 0.57470 0.69656 0.61709 0.87467 0.92895 0.88898 0.92037 0.85347 0.95797 0.93117 0.95169 0.80299 Entamoeba 0.49653 0.50963 0.50656 0.51965 0.50103 0.48614 0.46938 0.49731 0.46482 0.48025 0.47711 0.45704 0.46957 0.47807 0.48556 0.56794 0.45903 0.46017 0.56064 0.54287 0.54915 0.57470 0.00000 0.57675 0.51540 0.80855 0.95868 0.80567 0.84849 0.85323 0.87599 0.87694 0.94792 0.82265 Plasmodium 0.57674 0.56288 0.57882 0.58085 0.57628 0.56988 0.54345 0.56763 0.55614 0.59844 0.61166 0.58963 0.59809 0.59989 0.60025 0.68445 0.56945 0.59019 0.69706 0.68761 0.66459 0.69656 0.57675 0.00000 0.57474 0.83937 1.04218 0.96890 0.95832 0.96945 1.00138 0.99353 1.00666 0.84384 Trypanosom 0.48325 0.46590 0.47704 0.46222 0.48159 0.46296 0.44558 0.47674 0.46360 0.50096 0.49353 0.51111 0.48675 0.49218 0.48281 0.55976 0.52011 0.52553 0.61684 0.60873 0.56376 0.61709 0.51540 0.57474 0.00000 0.85468 0.96557 0.87501 0.91595 0.84479 0.94750 0.97294 0.90726 0.86857 Giardia 0.80743 0.79544 0.82323 0.80866 0.82072 0.79937 0.78785 0.81395 0.74670 0.84795 0.84970 0.82282 0.84123 0.84850 0.83917 0.92849 0.81052 0.83661 0.85448 0.86834 0.85892 0.87467 0.80855 0.83937 0.85468 0.00000 1.10516 1.01675 1.01259 0.99040 1.11588 1.07642 1.14990 0.99073 Sulfolobus 0.96143 0.97465 0.98082 0.97126 0.96858 1.00285 0.97744 0.99128 0.91518 1.00298 1.00338 0.95749 0.99433 1.00043 0.98423 1.08710 0.97457 0.98202 0.96891 0.97921 1.07433 0.92895 0.95868 1.04218 0.96557 1.10516 0.00000 0.85845 0.86593 0.69854 0.88757 0.88838 0.86794 0.77503 BMethanosa 0.88016 0.87610 0.88134 0.90073 0.88577 0.89388 0.88931 0.92719 0.79463 0.88763 0.89364 0.87546 0.87690 0.88919 0.88403 0.97950 0.85356 0.88082 0.90989 0.89529 0.94976 0.88898 0.80567 0.96890 0.87501 1.01675 0.85845 0.00000 0.14409 0.57441 0.54572 0.53082 0.74195 0.62035 MMethanosa 0.88740 0.88328 0.87873 0.90399 0.88634 0.90547 0.87804 0.90509 0.82175 0.89248 0.90407 0.89243 0.88924 0.89519 0.89657 0.98667 0.86137 0.90140 0.92923 0.90546 0.97260 0.92037 0.84849 0.95832 0.91595 1.01259 0.86593 0.14409 0.00000 0.60232 0.55017 0.56610 0.73219 0.66172 jMethanoco 0.83552 0.84043 0.83557 0.84841 0.83936 0.83883 0.82074 0.84737 0.78339 0.82688 0.84035 0.82242 0.82439 0.83487 0.83647 0.91380 0.82148 0.84273 0.87082 0.84611 0.91881 0.85347 0.85323 0.96945 0.84479 0.99040 0.69854 0.57441 0.60232 0.00000 0.64070 0.64457 0.60414 0.60702 Haloferax 0.92238 0.92141 0.93433 0.95424 0.92866 0.91371 0.89821 0.91679 0.88216 0.90157 0.90341 0.90931 0.89182 0.90049 0.90418 0.98743 0.90215 0.91530 1.00256 0.98637 1.00828 0.95797 0.87599 1.00138 0.94750 1.11588 0.88757 0.54572 0.55017 0.64070 0.00000 0.20795 0.74132 0.66123 Halobact 0.96109 0.96693 0.97713 0.95737 0.97092 0.95960 0.91055 0.93824 0.88949 0.93772 0.94919 0.92685 0.93543 0.94431 0.94624 1.04379 0.91814 0.96722 1.00671 0.98960 1.00784 0.93117 0.87694 0.99353 0.97294 1.07642 0.88838 0.53082 0.56610 0.64457 0.20795 0.00000 0.72893 0.71310 Enterococc 0.93653 0.95415 0.93675 0.94491 0.94571 0.95428 0.92224 0.93128 0.85984 0.93266 0.93455 0.90947 0.91747 0.92002 0.91706 0.97941 0.89540 0.90745 0.96299 0.96413 1.06313 0.95169 0.94792 1.00666 0.90726 1.14990 0.86794 0.74195 0.73219 0.60414 0.74132 0.72893 0.00000 0.77210 Thermus 0.83162 0.84506 0.84231 0.85364 0.83118 0.85625 0.85115 0.87557 0.78463 0.89078 0.89147 0.87490 0.87641 0.87967 0.87566 0.97273 0.87668 0.91149 0.86239 0.85822 0.86941 0.80299 0.82265 0.84384 0.86857 0.99073 0.77503 0.62035 0.66172 0.60702 0.66123 0.71310 0.77210 0.00000 Average distance (over all possible pairs of sequences): 0.63440 LIKELIHOOD MAPPING ANALYSIS Number of quartets: 1000 (random choice) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. Sequences are grouped in 4 clusters. Cluster a: 4 sequences Daucus Cyanidium Manduca Candida Cluster b: 1 sequences Plasmodium Cluster c: 1 sequences Giardia Cluster d: 3 sequences Sulfolobus BMethanosa MMethanosa Quartets of sequences used in the likelihood mapping analysis are generated by drawing one sequence from each of the clusters a, b, c, and d. LIKELIHOOD MAPPING STATISTICS Occupancies of the three areas 1, 2, 3: (a,b)-(c,d) /\ / \ / \ / 1 \ / \ / \ / \ / \ / \/ \ / 3 : 2 \ / : \ /__________________\ (a,d)-(b,c) (a,c)-(b,d) Number of quartets in region 1: 1000 (= 100.0%) Number of quartets in region 2: 0 (= 0.0%) Number of quartets in region 3: 0 (= 0.0%) Occupancies of the seven areas 1, 2, 3, 4, 5, 6, 7: (a,b)-(c,d) /\ / \ / 1 \ / \ / \ / /\ \ / 6 / \ 4 \ / / 7 \ \ / \ /______\ / \ / 3 : 5 : 2 \ /__________________\ (a,d)-(b,c) (a,c)-(b,d) Number of quartets in region 1: 1000 (= 100.0%) left: 159 right: 841 Number of quartets in region 2: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 3: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 4: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 5: 0 (= 0.0%) left: 0 right: 0 Number of quartets in region 6: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 7: 0 (= 0.0%) TIME STAMP Date and time: Mon Mar 02 12:13:19 1998 Runtime: 264 seconds (= 4.4 minutes = 0.1 hours)