PUZZLE 4.0.2 Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: 1st user tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 29 sequences with 744 amino acid sites Number of constant sites: 8 (= 1.1% 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) = 5.6% pi(N) = 3.6% pi(D) = 5.6% pi(C) = 1.4% pi(Q) = 3.6% pi(E) = 8.7% pi(G) = 6.4% pi(H) = 2.3% pi(I) = 6.6% pi(L) = 8.7% pi(K) = 7.0% pi(M) = 2.2% pi(F) = 4.3% pi(P) = 4.6% pi(S) = 5.0% pi(T) = 4.9% pi(W) = 1.6% pi(Y) = 3.7% pi(V) = 6.9% RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 1.83 (S.E. 0.08) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.1897 0.1250 2 0.3853 0.1250 3 0.5620 0.1250 4 0.7474 0.1250 5 0.9586 0.1250 6 1.2210 0.1250 7 1.5939 0.1250 8 2.3421 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.55. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming 1st user tree): 2 6 2 7 8 7 8 7 3 6 2 6 7 3 8 2 8 2 2 4 7 2 8 8 8 8 3 2 5 6 6 1 2 5 3 2 6 3 2 2 4 3 3 7 1 1 3 6 3 3 1 5 4 4 6 3 1 4 3 7 4 1 3 7 4 2 4 8 5 3 1 6 5 2 3 8 7 8 8 8 8 8 7 8 1 8 8 1 8 1 8 8 8 8 8 7 2 2 5 1 3 4 3 1 6 2 3 2 5 5 4 3 6 3 2 2 4 1 4 5 5 2 3 6 7 1 8 1 2 5 5 2 2 4 5 1 8 2 4 4 5 4 4 4 5 2 2 1 1 1 1 1 5 2 2 6 4 5 5 5 7 6 6 6 1 2 3 3 1 1 6 5 5 1 1 1 4 3 1 2 1 2 1 4 1 1 1 3 1 2 2 1 3 1 1 1 4 3 1 1 1 1 1 1 2 2 5 5 8 7 4 2 8 8 3 2 7 7 4 7 6 3 1 5 7 2 4 7 4 6 2 4 2 5 4 4 7 2 7 1 2 3 2 2 2 1 1 1 1 7 7 1 5 1 2 4 3 5 3 6 4 1 1 3 3 3 3 6 4 4 4 2 5 2 3 2 1 3 2 5 2 5 6 6 7 8 1 7 7 7 8 8 8 8 8 8 7 8 8 8 7 3 7 1 7 5 7 3 8 6 8 5 6 4 3 5 5 5 7 2 4 5 6 5 8 8 5 7 1 7 7 7 1 7 6 6 6 4 4 3 7 4 5 1 3 2 5 5 3 5 8 7 8 7 8 7 8 8 8 6 3 6 4 4 3 1 2 1 5 6 3 3 3 6 1 5 8 3 4 3 8 8 8 7 8 8 8 5 4 8 8 1 1 7 1 5 1 7 7 7 7 1 8 6 5 3 5 8 8 8 7 7 8 8 4 2 3 2 4 3 5 7 8 6 8 8 6 5 8 8 8 1 8 7 5 7 7 1 1 7 3 7 7 7 7 7 3 1 5 3 7 1 7 6 6 8 8 7 7 3 6 5 6 7 8 5 8 6 5 6 5 6 4 6 8 8 6 8 4 5 7 7 5 4 8 8 2 1 6 8 8 8 8 8 8 6 3 6 3 7 5 7 2 7 3 5 6 7 7 4 6 3 6 4 3 7 8 7 2 4 2 1 1 1 2 1 3 4 2 1 3 3 1 4 5 6 5 5 4 6 5 7 3 2 5 4 7 8 6 1 8 1 8 8 7 8 2 4 5 3 5 3 4 8 3 4 2 7 5 5 4 4 4 4 6 6 5 3 5 3 5 5 7 5 5 7 7 5 5 1 1 5 8 4 8 5 6 7 8 3 7 5 7 6 1 7 7 8 6 7 8 6 4 7 7 6 1 4 6 7 5 8 7 6 2 7 5 7 3 2 7 7 4 1 2 5 5 6 3 7 7 5 8 1 8 8 1 7 7 7 1 5 2 4 4 2 3 3 3 2 1 6 2 8 6 6 5 8 5 8 5 8 8 8 8 6 8 6 3 3 6 8 8 1 8 1 8 4 7 6 8 6 8 7 8 8 8 7 7 8 8 7 8 6 6 6 6 5 8 8 8 7 5 8 8 8 6 2 5 8 6 8 8 8 8 1 6 8 1 4 8 8 1 1 7 1 1 7 7 7 7 7 7 7 SEQUENCES IN INPUT ORDER 5% chi-square test p-value Aquifex failed 4.51% Thermotoga passed 7.93% Bacillus passed 33.45% Treponema failed 0.00% Escherichi passed 25.52% Haemophilu passed 48.27% Rickettsia failed 0.06% Zymomonas failed 0.89% Synechocys passed 27.26% tMycobacte failed 0.00% Chlamydia passed 12.22% Helicobact failed 0.87% 2Saccharom failed 0.01% Candida failed 0.00% Drosophila passed 49.44% Homo passed 84.71% Caenorhabd passed 62.27% Saccharomy passed 74.51% Deinococcu passed 35.92% lMycobacte failed 0.06% Borellia failed 0.13% Methanococ failed 0.01% Methanobac failed 0.81% Archaeoglo passed 23.34% Pyrococcus failed 1.51% Sulfolobus passed 39.14% Aeropyrum failed 0.00% pMycoplasm failed 0.00% gMycoplasm failed 0.00% 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. 29 Aquifex 0.00000 1.02772 1.07840 1.58205 1.33043 1.31693 1.40654 1.35650 1.36712 1.57157 1.72483 1.62932 2.34709 2.34201 6.28163 6.36710 6.48830 6.51389 5.87727 5.56844 6.05725 5.12785 5.17779 5.41727 5.48030 5.03472 5.58305 6.01309 6.96748 Thermotoga 1.02772 0.00000 1.00960 1.35849 1.20433 1.21157 1.42565 1.46366 1.34735 1.62811 1.70362 1.60195 2.78846 2.73472 6.50556 6.09933 6.23202 5.44336 5.15639 4.94886 5.48936 5.04083 5.11613 5.69212 4.93657 5.07336 5.15305 6.32187 7.48450 Bacillus 1.07840 1.00960 0.00000 1.26819 1.00478 1.03105 1.27975 1.28984 1.25078 1.50560 1.53038 1.59321 2.58540 2.50612 5.82653 5.46928 5.54341 5.07787 5.09105 5.04319 5.55889 5.03312 4.65124 4.82398 4.99375 4.89240 4.74092 5.25644 5.66379 Treponema 1.58205 1.35849 1.26819 0.00000 1.49288 1.52157 1.90775 1.75861 1.79659 1.72718 1.86495 1.94540 2.96504 2.64062 6.57955 6.21971 6.38087 6.04521 5.12230 5.33392 6.59925 4.59055 4.98191 4.99775 4.63794 4.97118 4.62333 5.72679 6.34595 Escherichi 1.33043 1.20433 1.00478 1.49288 0.00000 0.32064 1.11454 1.10233 1.17651 1.49643 1.63695 1.59753 2.37987 2.44072 5.81963 5.68565 5.75587 5.51419 5.21784 4.74384 5.23353 5.00916 4.95062 5.00899 4.75833 4.88305 4.72133 5.56954 5.80131 Haemophilu 1.31693 1.21157 1.03105 1.52157 0.32064 0.00000 1.15117 1.06589 1.24178 1.49955 1.67578 1.62636 2.42790 2.52949 5.77688 5.81764 5.85613 5.30450 5.15257 4.83559 5.33222 4.79497 4.76633 4.93414 4.84994 5.00612 4.74318 5.90670 6.31797 Rickettsia 1.40654 1.42565 1.27975 1.90775 1.11454 1.15117 0.00000 0.97286 1.48838 1.59707 2.17366 1.73317 2.16801 2.33088 6.39702 6.57775 6.55882 6.22654 6.65953 5.71365 7.30025 5.41012 5.82366 5.73306 5.29000 5.46905 5.64326 6.85631 7.66298 Zymomonas 1.35650 1.46366 1.28984 1.75861 1.10233 1.06589 0.97286 0.00000 1.26090 1.67963 2.07034 1.92964 2.41250 2.64367 5.87257 6.83916 7.10405 6.45652 5.77157 6.02919 6.83553 5.57743 5.15535 5.91442 5.13021 5.96520 5.38601 5.56798 6.55525 Synechocys 1.36712 1.34735 1.25078 1.79659 1.17651 1.24178 1.48838 1.26090 0.00000 1.58140 1.97503 1.68937 2.65493 2.63791 6.12078 6.45129 6.20502 6.23721 5.66141 5.20963 5.75124 5.28097 5.32913 5.58141 5.01247 5.42650 5.49969 6.01882 7.13580 tMycobacte 1.57157 1.62811 1.50560 1.72718 1.49643 1.49955 1.59707 1.67963 1.58140 0.00000 1.91991 2.00078 2.49848 2.42539 6.24646 6.60013 6.27688 6.63001 5.36224 5.35343 6.69547 5.32947 4.84127 4.86702 4.47932 5.02319 4.95911 6.31110 6.56956 Chlamydia 1.72483 1.70362 1.53038 1.86495 1.63695 1.67578 2.17366 2.07034 1.97503 1.91991 0.00000 1.94500 2.90893 2.85123 6.66393 6.19863 6.42759 5.68305 5.67760 5.25848 5.50422 4.51570 4.73255 5.02260 5.02366 4.81494 4.86291 7.40824 7.93922 Helicobact 1.62932 1.60195 1.59321 1.94540 1.59753 1.62636 1.73317 1.92964 1.68937 2.00078 1.94500 0.00000 2.50617 2.62878 6.03159 5.74421 5.79611 5.81445 5.67002 5.23675 6.24497 4.98898 5.12337 5.76700 5.16890 4.95905 5.41116 6.50923 7.83224 2Saccharom 2.34709 2.78846 2.58540 2.96504 2.37987 2.42790 2.16801 2.41250 2.65493 2.49848 2.90893 2.50617 0.00000 1.27211 7.00766 7.13018 7.07031 7.37672 6.48316 6.90785 6.63929 5.64275 6.22901 5.45180 5.54783 5.50815 5.40908 7.05143 6.76268 Candida 2.34201 2.73472 2.50612 2.64062 2.44072 2.52949 2.33088 2.64367 2.63791 2.42539 2.85123 2.62878 1.27211 0.00000 6.72539 6.86235 6.52429 6.63164 5.69228 6.34896 6.50129 6.16692 6.16159 5.80899 6.42648 5.19543 5.80494 7.57564 7.76333 Drosophila 6.28163 6.50556 5.82653 6.57955 5.81963 5.77688 6.39702 5.87257 6.12078 6.24646 6.66393 6.03159 7.00766 6.72539 0.00000 0.48088 0.58228 0.75855 1.55764 1.39498 1.52525 1.84920 1.84530 1.98908 1.82964 2.14462 2.20746 2.31062 2.51848 Homo 6.36710 6.09933 5.46928 6.21971 5.68565 5.81764 6.57775 6.83916 6.45129 6.60013 6.19863 5.74421 7.13018 6.86235 0.48088 0.00000 0.63277 0.76824 1.55364 1.30152 1.52877 1.73634 1.80785 1.95001 1.74336 1.98740 2.20653 2.42456 2.54280 Caenorhabd 6.48830 6.23202 5.54341 6.38087 5.75587 5.85613 6.55882 7.10405 6.20502 6.27688 6.42759 5.79611 7.07031 6.52429 0.58228 0.63277 0.00000 0.76373 1.63022 1.40915 1.34100 1.75150 1.82339 1.94787 1.71765 2.04814 2.10104 2.10934 2.39433 Saccharomy 6.51389 5.44336 5.07787 6.04521 5.51419 5.30450 6.22654 6.45652 6.23721 6.63001 5.68305 5.81445 7.37672 6.63164 0.75855 0.76824 0.76373 0.00000 1.59513 1.33425 1.44636 1.88943 1.88440 2.06115 1.88358 2.05012 2.07430 2.19700 2.38058 Deinococcu 5.87727 5.15639 5.09105 5.12230 5.21784 5.15257 6.65953 5.77157 5.66141 5.36224 5.67760 5.67002 6.48316 5.69228 1.55764 1.55364 1.63022 1.59513 0.00000 0.95968 1.30343 2.01086 1.94140 1.96601 1.75534 1.97329 1.97467 2.24848 2.40235 lMycobacte 5.56844 4.94886 5.04319 5.33392 4.74384 4.83559 5.71365 6.02919 5.20963 5.35343 5.25848 5.23675 6.90785 6.34896 1.39498 1.30152 1.40915 1.33425 0.95968 0.00000 1.18571 1.95592 1.80724 2.00217 1.70831 2.07502 1.84520 2.36923 2.20941 Borellia 6.05725 5.48936 5.55889 6.59925 5.23353 5.33222 7.30025 6.83553 5.75124 6.69547 5.50422 6.24497 6.63929 6.50129 1.52525 1.52877 1.34100 1.44636 1.30343 1.18571 0.00000 1.92491 2.13735 2.02937 1.79926 1.78973 1.82812 2.01882 2.24429 Methanococ 5.12785 5.04083 5.03312 4.59055 5.00916 4.79497 5.41012 5.57743 5.28097 5.32947 4.51570 4.98898 5.64275 6.16692 1.84920 1.73634 1.75150 1.88943 2.01086 1.95592 1.92491 0.00000 0.74299 0.94215 1.00080 0.99003 1.02264 2.71916 2.87297 Methanobac 5.17779 5.11613 4.65124 4.98191 4.95062 4.76633 5.82366 5.15535 5.32913 4.84127 4.73255 5.12337 6.22901 6.16159 1.84530 1.80785 1.82339 1.88440 1.94140 1.80724 2.13735 0.74299 0.00000 0.85600 0.98023 1.10820 1.06815 2.78603 2.97018 Archaeoglo 5.41727 5.69212 4.82398 4.99775 5.00899 4.93414 5.73306 5.91442 5.58141 4.86702 5.02260 5.76700 5.45180 5.80899 1.98908 1.95001 1.94787 2.06115 1.96601 2.00217 2.02937 0.94215 0.85600 0.00000 1.02089 1.22378 1.16175 2.86790 3.16538 Pyrococcus 5.48030 4.93657 4.99375 4.63794 4.75833 4.84994 5.29000 5.13021 5.01247 4.47932 5.02366 5.16890 5.54783 6.42648 1.82964 1.74336 1.71765 1.88358 1.75534 1.70831 1.79926 1.00080 0.98023 1.02089 0.00000 1.02685 0.93918 2.59400 2.84915 Sulfolobus 5.03472 5.07336 4.89240 4.97118 4.88305 5.00612 5.46905 5.96520 5.42650 5.02319 4.81494 4.95905 5.50815 5.19543 2.14462 1.98740 2.04814 2.05012 1.97329 2.07502 1.78973 0.99003 1.10820 1.22378 1.02685 0.00000 0.72156 2.71596 3.06469 Aeropyrum 5.58305 5.15305 4.74092 4.62333 4.72133 4.74318 5.64326 5.38601 5.49969 4.95911 4.86291 5.41116 5.40908 5.80494 2.20746 2.20653 2.10104 2.07430 1.97467 1.84520 1.82812 1.02264 1.06815 1.16175 0.93918 0.72156 0.00000 2.56614 2.89728 pMycoplasm 6.01309 6.32187 5.25644 5.72679 5.56954 5.90670 6.85631 5.56798 6.01882 6.31110 7.40824 6.50923 7.05143 7.57564 2.31062 2.42456 2.10934 2.19700 2.24848 2.36923 2.01882 2.71916 2.78603 2.86790 2.59400 2.71596 2.56614 0.00000 0.54569 gMycoplasm 6.96748 7.48450 5.66379 6.34595 5.80131 6.31797 7.66298 6.55525 7.13580 6.56956 7.93922 7.83224 6.76268 7.76333 2.51848 2.54280 2.39433 2.38058 2.40235 2.20941 2.24429 2.87297 2.97018 3.16538 2.84915 3.06469 2.89728 0.54569 0.00000 Average distance (over all possible pairs of sequences): 3.84307 TREE SEARCH 1 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. :-28 pMycoplasm :------30 : :--29 gMycoplasm :--37 : : :-15 Drosophila : : :-31 : : : :-16 Homo : : :-32 : : : :--17 Caenorhabd : : :--33 : : : :--18 Saccharomy : :-36 : : :--19 Deinococcu : : :-34 : : : :--20 lMycobacte : :-35 : :---21 Borellia :---------------42 : : :--26 Sulfolobus : : :-38 : : : :--27 Aeropyrum : :-41 : : :--23 Methanobac : : :-39 : : : :--24 Archaeoglo : :-40 : : :--22 Methanococ : : : :--25 Pyrococcus : : :-5 Escherichi :--43 : :-6 Haemophilu : : :---13 2Saccharom :------44 : :---14 Candida : : :--7 Rickettsia :--45 : :--8 Zymomonas : :---2 Thermotoga : :--3 Bacillus : :----4 Treponema : :---9 Synechocys : :----10 tMycobacte : :-----11 Chlamydia : :----12 Helicobact : :---1 Aquifex branch length S.E. branch length S.E. Aquifex 1 0.64982 0.05472 30 1.52973 0.14056 Thermotoga 2 0.61013 0.05234 31 0.11108 0.02848 Bacillus 3 0.53997 0.04784 32 0.15544 0.03586 Treponema 4 0.97058 0.07345 33 0.38163 0.05895 Escherichi 5 0.14676 0.02320 34 0.26487 0.05304 Haemophilu 6 0.17035 0.02420 35 0.16889 0.04796 Rickettsia 7 0.56800 0.06468 36 0.09812 0.05237 Zymomonas 8 0.47748 0.06009 37 0.52044 0.08035 Synechocys 9 0.83163 0.06515 38 0.23340 0.04177 tMycobacte 10 1.13178 0.08360 39 0.11219 0.03422 Chlamydia 11 1.19778 0.08782 40 0.18698 0.04083 Helicobact 12 1.13109 0.08305 41 0.19441 0.07236 2Saccharom 13 0.62765 0.07665 42 4.23379 0.40922 Candida 14 0.65180 0.07840 43 0.50624 0.04841 Drosophila 15 0.24624 0.03333 44 1.49965 0.13339 Homo 16 0.28464 0.03531 45 0.49072 0.06290 Caenorhabd 17 0.34367 0.04075 Saccharomy 18 0.39519 0.04672 Deinococcu 19 0.59190 0.06408 lMycobacte 20 0.47067 0.05742 Borellia 21 0.63727 0.06783 Methanococ 22 0.46763 0.05265 Methanobac 23 0.37210 0.04686 Archaeoglo 24 0.57970 0.05885 Pyrococcus 25 0.45989 0.05079 Sulfolobus 26 0.38678 0.04618 Aeropyrum 27 0.39954 0.04652 pMycoplasm 28 0.14705 0.04154 20 iterations until convergence gMycoplasm 29 0.43732 0.04786 log L: -28653.29 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Aquifex:0.64982,(((pMycoplasm:0.14705,gMycoplasm:0.43732):1.52973, ((((Drosophila:0.24624,Homo:0.28464):0.11108,Caenorhabd:0.34367) :0.15544,Saccharomy:0.39519):0.38163,((Deinococcu:0.59190,lMycobacte:0.47067) :0.26487,Borellia:0.63727):0.16889):0.09812):0.52044,((Sulfolobus:0.38678, Aeropyrum:0.39954):0.23340,((Methanobac:0.37210,Archaeoglo:0.57970) :0.11219,Methanococ:0.46763):0.18698,Pyrococcus:0.45989):0.19441) :4.23379,(Escherichi:0.14676,Haemophilu:0.17035):0.50624,(2Saccharom:0.62765, Candida:0.65180):1.49965,(Rickettsia:0.56800,Zymomonas:0.47748) :0.49072,Thermotoga:0.61013,Bacillus:0.53997,Treponema:0.97058,Synechocys:0.83163, tMycobacte:1.13178,Chlamydia:1.19778,Helicobact:1.13109); TIME STAMP Date and time: Thu Feb 03 09:48:30 2000 Runtime: 1062 seconds (= 17.7 minutes = 0.3 hours)