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: 28 sequences with 715 amino acid sites Number of constant sites: 158 (= 22.1% 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) = 5.1% pi(N) = 3.3% pi(D) = 5.7% pi(C) = 1.1% pi(Q) = 3.3% pi(E) = 7.1% pi(G) = 8.3% pi(H) = 1.2% pi(I) = 6.0% pi(L) = 8.4% pi(K) = 5.6% pi(M) = 3.1% pi(F) = 3.7% pi(P) = 5.0% pi(S) = 7.1% pi(T) = 5.7% pi(W) = 1.0% pi(Y) = 4.1% pi(V) = 7.8% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value Eremotheci passed 98.78% Saccharomy passed 99.06% Candida passed 99.81% Neurospora passed 59.10% Schizosacc passed 97.48% Homo1 passed 99.99% Bos1 passed 100.00% A1Gallus passed 100.00% Manduca passed 99.99% Drosophila passed 99.88% Ascidia passed 98.17% Dictyostel passed 61.12% 1Acetabula passed 99.99% 2Acetabula passed 99.99% Scherffeli passed 97.72% Daucus passed 99.52% Brassica passed 99.09% Arabidopsi passed 99.03% Vigna passed 99.49% Gossypium passed 95.99% Beta passed 99.33% Cyanidium passed 99.80% Trypanosom passed 98.52% Trichomona passed 99.76% Plasmodium passed 81.94% Entamoeba passed 99.65% Nosema passed 71.54% Giardia passed 33.60% 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. 28 Eremotheci 0.00000 0.10736 0.13149 0.35282 0.45329 0.49605 0.48934 0.50338 0.46003 0.53100 0.50531 0.53691 0.56265 0.54902 0.61462 0.59972 0.59090 0.59226 0.59640 0.59229 0.59475 0.53039 0.62653 0.63370 0.69690 0.55162 0.63929 0.85607 Saccharomy 0.10736 0.00000 0.13648 0.32663 0.44621 0.49373 0.49998 0.51105 0.48003 0.53079 0.51205 0.52107 0.54787 0.53985 0.60299 0.57790 0.56496 0.57823 0.57424 0.57812 0.58338 0.53415 0.61575 0.63808 0.69997 0.56106 0.62689 0.85974 Candida 0.13149 0.13648 0.00000 0.32802 0.42784 0.49185 0.48630 0.49929 0.46215 0.52594 0.48608 0.56402 0.55709 0.54754 0.61521 0.61029 0.60206 0.60324 0.60113 0.60743 0.59407 0.52804 0.60699 0.60827 0.68764 0.54068 0.61862 0.86735 Neurospora 0.35282 0.32663 0.32802 0.00000 0.43832 0.51445 0.50822 0.52128 0.49872 0.55263 0.49143 0.56260 0.56583 0.54638 0.60183 0.55837 0.56340 0.56662 0.55960 0.55725 0.57109 0.52391 0.60347 0.62480 0.69770 0.57169 0.59489 0.87396 Schizosacc 0.45329 0.44621 0.42784 0.43832 0.00000 0.47613 0.46928 0.47721 0.50155 0.51679 0.47157 0.53295 0.54112 0.51816 0.58508 0.58828 0.59041 0.59221 0.58451 0.58591 0.58724 0.51517 0.55934 0.60443 0.66460 0.54515 0.63145 0.85138 Homo1 0.49605 0.49373 0.49185 0.51445 0.47613 0.00000 0.01953 0.05478 0.20330 0.22526 0.24746 0.41756 0.44233 0.41604 0.46563 0.43089 0.42841 0.43351 0.41652 0.41447 0.42203 0.38569 0.49311 0.57701 0.61684 0.47600 0.57842 0.82683 Bos1 0.48934 0.49998 0.48630 0.50822 0.46928 0.01953 0.00000 0.04121 0.19144 0.21337 0.24156 0.40584 0.44095 0.41229 0.45649 0.43355 0.42933 0.42897 0.41899 0.41240 0.41984 0.36923 0.48638 0.56099 0.60323 0.46849 0.56282 0.81889 A1Gallus 0.50338 0.51105 0.49929 0.52128 0.47721 0.05478 0.04121 0.00000 0.20979 0.22389 0.25042 0.40159 0.45278 0.42633 0.45817 0.43514 0.43109 0.43259 0.42283 0.41344 0.42310 0.38372 0.48475 0.57036 0.60341 0.48430 0.57324 0.82152 Manduca 0.46003 0.48003 0.46215 0.49872 0.50155 0.20330 0.19144 0.20979 0.00000 0.15753 0.26902 0.39931 0.41697 0.39680 0.45630 0.42991 0.43056 0.42203 0.41920 0.42429 0.42307 0.41113 0.52041 0.53621 0.57038 0.45805 0.54407 0.79347 Drosophila 0.53100 0.53079 0.52594 0.55263 0.51679 0.22526 0.21337 0.22389 0.15753 0.00000 0.28631 0.42826 0.45870 0.44548 0.51940 0.46809 0.46817 0.45924 0.46442 0.45986 0.46193 0.44702 0.53279 0.56965 0.62076 0.47872 0.57013 0.85130 Ascidia 0.50531 0.51205 0.48608 0.49143 0.47157 0.24746 0.24156 0.25042 0.26902 0.28631 0.00000 0.43644 0.43618 0.41422 0.48160 0.44709 0.45373 0.45652 0.46148 0.45385 0.44913 0.42393 0.50801 0.54936 0.59726 0.49649 0.59683 0.84545 Dictyostel 0.53691 0.52107 0.56402 0.56260 0.53295 0.41756 0.40584 0.40159 0.39931 0.42826 0.43644 0.00000 0.47764 0.45372 0.51567 0.48840 0.48454 0.47593 0.47651 0.47535 0.48481 0.41139 0.48750 0.55809 0.56486 0.46293 0.59915 0.80361 1Acetabula 0.56265 0.54787 0.55709 0.56583 0.54112 0.44233 0.44095 0.45278 0.41697 0.45870 0.43618 0.47764 0.00000 0.04901 0.29916 0.30502 0.30672 0.29687 0.31201 0.31343 0.31105 0.37492 0.48206 0.59669 0.56940 0.49499 0.63544 0.79481 2Acetabula 0.54902 0.53985 0.54754 0.54638 0.51816 0.41604 0.41229 0.42633 0.39680 0.44548 0.41422 0.45372 0.04901 0.00000 0.28446 0.31308 0.31190 0.30157 0.31433 0.30214 0.30329 0.36304 0.44930 0.56395 0.54524 0.46796 0.61229 0.76780 Scherffeli 0.61462 0.60299 0.61521 0.60183 0.58508 0.46563 0.45649 0.45817 0.45630 0.51940 0.48160 0.51567 0.29916 0.28446 0.00000 0.35607 0.35464 0.35333 0.33972 0.34599 0.36084 0.40091 0.51462 0.61896 0.59611 0.51516 0.62516 0.80255 Daucus 0.59972 0.57790 0.61029 0.55837 0.58828 0.43089 0.43355 0.43514 0.42991 0.46809 0.44709 0.48840 0.30502 0.31308 0.35607 0.00000 0.03013 0.06110 0.05014 0.04513 0.06624 0.36292 0.49751 0.59550 0.58117 0.49654 0.59570 0.79520 Brassica 0.59090 0.56496 0.60206 0.56340 0.59041 0.42841 0.42933 0.43109 0.43056 0.46817 0.45373 0.48454 0.30672 0.31190 0.35464 0.03013 0.00000 0.03834 0.05942 0.05806 0.07828 0.35332 0.49581 0.58664 0.58062 0.50104 0.59249 0.81154 Arabidopsi 0.59226 0.57823 0.60324 0.56662 0.59221 0.43351 0.42897 0.43259 0.42203 0.45924 0.45652 0.47593 0.29687 0.30157 0.35333 0.06110 0.03834 0.00000 0.07343 0.06635 0.10008 0.36124 0.48026 0.57326 0.57287 0.49852 0.59249 0.80834 Vigna 0.59640 0.57424 0.60113 0.55960 0.58451 0.41652 0.41899 0.42283 0.41920 0.46442 0.46148 0.47651 0.31201 0.31433 0.33972 0.05014 0.05942 0.07343 0.00000 0.05220 0.07900 0.35558 0.49131 0.58416 0.58314 0.50655 0.59994 0.80838 Gossypium 0.59229 0.57812 0.60743 0.55725 0.58591 0.41447 0.41240 0.41344 0.42429 0.45986 0.45385 0.47535 0.31343 0.30214 0.34599 0.04513 0.05806 0.06635 0.05220 0.00000 0.07039 0.36356 0.48003 0.57831 0.56731 0.50964 0.58452 0.78343 Beta 0.59475 0.58338 0.59407 0.57109 0.58724 0.42203 0.41984 0.42310 0.42307 0.46193 0.44913 0.48481 0.31105 0.30329 0.36084 0.06624 0.07828 0.10008 0.07900 0.07039 0.00000 0.35787 0.47634 0.59100 0.58530 0.51964 0.60296 0.79647 Cyanidium 0.53039 0.53415 0.52804 0.52391 0.51517 0.38569 0.36923 0.38372 0.41113 0.44702 0.42393 0.41139 0.37492 0.36304 0.40091 0.36292 0.35332 0.36124 0.35558 0.36356 0.35787 0.00000 0.46276 0.52990 0.55450 0.45801 0.57058 0.73988 Trypanosom 0.62653 0.61575 0.60699 0.60347 0.55934 0.49311 0.48638 0.48475 0.52041 0.53279 0.50801 0.48750 0.48206 0.44930 0.51462 0.49751 0.49581 0.48026 0.49131 0.48003 0.47634 0.46276 0.00000 0.55353 0.57050 0.51363 0.66842 0.82985 Trichomona 0.63370 0.63808 0.60827 0.62480 0.60443 0.57701 0.56099 0.57036 0.53621 0.56965 0.54936 0.55809 0.59669 0.56395 0.61896 0.59550 0.58664 0.57326 0.58416 0.57831 0.59100 0.52990 0.55353 0.00000 0.65932 0.55762 0.71009 0.83182 Plasmodium 0.69690 0.69997 0.68764 0.69770 0.66460 0.61684 0.60323 0.60341 0.57038 0.62076 0.59726 0.56486 0.56940 0.54524 0.59611 0.58117 0.58062 0.57287 0.58314 0.56731 0.58530 0.55450 0.57050 0.65932 0.00000 0.58235 0.75400 0.81614 Entamoeba 0.55162 0.56106 0.54068 0.57169 0.54515 0.47600 0.46849 0.48430 0.45805 0.47872 0.49649 0.46293 0.49499 0.46796 0.51516 0.49654 0.50104 0.49852 0.50655 0.50964 0.51964 0.45801 0.51363 0.55762 0.58235 0.00000 0.61587 0.79537 Nosema 0.63929 0.62689 0.61862 0.59489 0.63145 0.57842 0.56282 0.57324 0.54407 0.57013 0.59683 0.59915 0.63544 0.61229 0.62516 0.59570 0.59249 0.59249 0.59994 0.58452 0.60296 0.57058 0.66842 0.71009 0.75400 0.61587 0.00000 0.89032 Giardia 0.85607 0.85974 0.86735 0.87396 0.85138 0.82683 0.81889 0.82152 0.79347 0.85130 0.84545 0.80361 0.79481 0.76780 0.80255 0.79520 0.81154 0.80834 0.80838 0.78343 0.79647 0.73988 0.82985 0.83182 0.81614 0.79537 0.89032 0.00000 Average distance (over all possible pairs of sequences): 0.49324 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. :---------23 Trypanosom : :------------24 Trichomona : :------------25 Plasmodium : :----------26 Entamoeba : : :--------12 Dictyostel : :--38 : : : :------------27 Nosema : : : :---33 : : : : : :-------5 Schizosacc : : : : :---32 : : : : : :------4 Neurospora : : : : :----31 : : : : : :--3 Candida : : : : :----30 : : : : : :--1 Eremotheci : : : : :--29 : : : : :--2 Saccharomy : : :--37 : : : :------11 Ascidia : : :----36 : : : :-6 Homo1 : : :---34 : : : :-7 Bos1 : : : : : : : :--8 A1Gallus : : : : : : :---9 Manduca : : :--35 : : :---10 Drosophila :---46 : : :------22 Cyanidium : :--45 : : :------15 Scherffeli : : :---40 : : : : :--13 1Acetabula : : : :----39 : : : :-14 2Acetabula : :---44 : : :-21 Beta : :----43 : : :-19 Vigna : :-42 : :-20 Gossypium : : : : :-16 Daucus : :-41 : :-17 Brassica : : : :--18 Arabidopsi : :--------------------28 Giardia branch length S.E. branch length S.E. Eremotheci 1 0.05584 0.01039 29 0.03516 0.00989 Saccharomy 2 0.05616 0.01042 30 0.12240 0.01828 Candida 3 0.04960 0.01099 31 0.10063 0.01834 Neurospora 4 0.19561 0.02205 32 0.08013 0.01736 Schizosacc 5 0.22732 0.02391 33 0.08324 0.01701 Homo1 6 0.01661 0.00529 34 0.09038 0.01379 Bos1 7 0.00302 0.00242 35 0.06535 0.01237 A1Gallus 8 0.03836 0.00804 36 0.10197 0.01700 Manduca 9 0.07038 0.01220 37 0.06181 0.01518 Drosophila 10 0.09636 0.01398 38 0.05732 0.01425 Ascidia 11 0.17112 0.01866 39 0.11259 0.01647 Dictyostel 12 0.24039 0.02413 40 0.07570 0.01522 1Acetabula 13 0.04022 0.00864 41 0.02767 0.00797 2Acetabula 14 0.00901 0.00495 42 0.02639 0.00775 Scherffeli 15 0.17708 0.02018 43 0.12473 0.01777 Daucus 16 0.02463 0.00711 44 0.07533 0.01555 Brassica 17 0.00923 0.00542 45 0.05122 0.01409 Arabidopsi 18 0.03767 0.00850 46 0.08733 0.01667 Vigna 19 0.02971 0.00754 Gossypium 20 0.02687 0.00723 Beta 21 0.03087 0.00820 Cyanidium 22 0.18945 0.02140 Trypanosom 23 0.29801 0.02722 Trichomona 24 0.37877 0.03123 Plasmodium 25 0.38918 0.03172 Entamoeba 26 0.30285 0.02742 Nosema 27 0.39178 0.03258 13 iterations until convergence Giardia 28 0.64569 0.04463 log L: -16290.06 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia:0.64569,Trypanosom:0.29801,Trichomona:0.37877,Plasmodium:0.38918, Entamoeba:0.30285,((Dictyostel:0.24039,((Nosema:0.39178,(Schizosacc:0.22732, (Neurospora:0.19561,(Candida:0.04960,(Eremotheci:0.05584,Saccharomy:0.05616) :0.03516):0.12240):0.10063):0.08013):0.08324,(Ascidia:0.17112,(Homo1:0.01661, Bos1:0.00302,A1Gallus:0.03836):0.09038,(Manduca:0.07038,Drosophila:0.09636) :0.06535):0.10197):0.06181):0.05732,(Cyanidium:0.18945,((Scherffeli:0.17708, (1Acetabula:0.04022,2Acetabula:0.00901):0.11259):0.07570,(Beta:0.03087, (Vigna:0.02971,Gossypium:0.02687,(Daucus:0.02463,Brassica:0.00923, Arabidopsi:0.03767):0.02767):0.02639):0.12473):0.07533):0.05122):0.08733); TIME STAMP Date and time: Wed Mar 15 14:08:51 2000 Runtime: 46 seconds (= 0.8 minutes = 0.0 hours)