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: Gamma distributed rates Gamma distribution parameter alpha: 0.60 Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0146 0.1250 2 0.0938 0.1250 3 0.2304 0.1250 4 0.4318 0.1250 5 0.7208 0.1250 6 1.1492 0.1250 7 1.8561 0.1250 8 3.5033 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 1.67. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming 1st user tree): 1 6 8 8 7 7 8 8 8 8 8 8 8 8 7 7 8 8 7 8 8 8 5 7 8 8 4 8 5 8 6 3 3 4 8 8 4 2 1 6 2 6 6 3 8 1 6 5 2 4 1 3 3 6 1 1 6 8 7 1 3 1 1 2 1 3 3 5 5 4 6 3 3 2 1 2 1 1 3 1 5 1 5 7 3 4 1 6 1 7 5 2 7 6 4 1 3 2 5 3 3 1 1 5 6 7 6 1 6 1 1 2 2 2 1 1 7 8 1 6 8 8 5 8 4 8 8 8 8 8 8 4 5 1 3 4 1 5 6 6 7 6 3 6 6 8 8 8 5 8 3 8 3 8 8 8 8 8 8 8 8 8 8 6 3 3 7 6 5 5 1 1 4 8 3 8 3 8 1 3 7 4 6 8 8 4 7 5 5 7 5 1 1 4 1 1 1 8 8 1 1 4 1 1 3 7 5 7 3 8 7 5 6 7 5 3 7 7 3 7 1 6 7 8 5 1 1 8 6 6 6 7 2 5 6 8 3 7 7 8 8 8 7 5 8 5 7 4 1 2 1 7 5 3 3 4 7 6 3 6 7 6 6 7 3 3 6 2 1 1 1 4 1 1 6 3 3 1 7 3 4 1 3 1 5 3 1 3 1 2 1 1 1 1 1 1 2 3 1 1 3 4 1 1 7 2 1 2 2 6 3 5 1 2 1 1 1 1 1 1 1 1 1 3 1 3 1 6 5 1 1 5 3 5 7 7 7 8 8 7 5 7 8 8 8 7 7 8 5 7 4 1 7 6 5 5 2 2 6 1 1 7 3 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 5 1 3 6 1 1 4 1 7 3 4 5 2 4 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 2 1 2 2 4 1 3 1 1 3 1 6 3 3 1 2 4 1 1 1 2 3 1 6 3 8 4 6 1 5 3 2 1 8 1 1 8 1 2 8 8 4 8 1 1 1 8 8 1 1 1 1 8 1 8 8 8 8 1 8 1 8 1 2 3 5 3 2 3 1 1 1 1 4 3 1 1 4 3 1 1 3 1 2 5 4 1 3 6 3 2 1 2 1 1 1 1 3 1 3 1 1 2 2 1 1 3 1 2 3 3 3 6 4 1 5 1 3 3 8 7 6 1 6 7 8 5 7 8 8 8 6 7 7 4 7 8 6 3 7 6 6 6 6 4 3 3 8 3 5 7 4 7 4 3 3 1 1 1 1 5 4 3 1 5 4 7 4 2 5 5 4 4 5 3 6 7 4 5 5 3 4 1 4 1 1 5 6 3 8 1 1 7 8 3 1 6 7 1 3 7 8 2 6 6 4 6 6 6 5 7 7 7 5 7 7 5 5 6 8 7 7 8 8 7 8 7 6 7 4 5 5 8 7 8 3 7 7 8 6 8 7 7 8 8 8 6 7 5 5 1 3 7 5 4 7 5 7 4 6 8 8 7 8 8 8 8 8 7 5 8 8 7 5 8 8 7 3 6 7 6 7 7 7 8 7 8 8 8 8 8 8 8 8 8 8 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 0.11636 0.14512 0.47164 0.63380 0.69322 0.68634 0.71343 0.62142 0.73849 0.72110 0.77833 0.82253 0.79457 0.94358 0.89250 0.88331 0.88835 0.88264 0.88588 0.89461 0.76842 0.95751 0.97047 1.09169 0.82385 0.99785 1.44940 Saccharomy 0.11636 0.00000 0.15315 0.42534 0.62449 0.70110 0.71150 0.73615 0.65570 0.74352 0.72883 0.74941 0.79223 0.77592 0.91096 0.86258 0.84538 0.86915 0.85764 0.86794 0.88573 0.76555 0.94768 0.97385 1.10571 0.84098 0.97982 1.47369 Candida 0.14512 0.15315 0.00000 0.42813 0.58979 0.69069 0.68455 0.70955 0.62966 0.74121 0.68418 0.81793 0.81489 0.79621 0.94377 0.92101 0.91381 0.91891 0.90629 0.92315 0.90336 0.75875 0.92906 0.92264 1.08629 0.80406 0.95609 1.49698 Neurospora 0.47164 0.42534 0.42813 0.00000 0.59502 0.72747 0.71515 0.73726 0.68382 0.77994 0.68584 0.80959 0.83779 0.79725 0.91580 0.82748 0.83948 0.84573 0.83142 0.82926 0.85440 0.74304 0.88808 0.97142 1.07737 0.83637 0.90467 1.48151 Schizosacc 0.63380 0.62449 0.58979 0.59502 0.00000 0.66765 0.66068 0.67321 0.70424 0.74260 0.67221 0.76926 0.78047 0.74114 0.87674 0.88585 0.89229 0.89482 0.87396 0.88187 0.88986 0.73100 0.82803 0.91662 1.03069 0.80360 0.98500 1.43601 Homo1 0.69322 0.70110 0.69069 0.72747 0.66765 0.00000 0.01971 0.05654 0.23445 0.26788 0.29607 0.55528 0.59876 0.55274 0.65111 0.58300 0.58320 0.59115 0.55991 0.56018 0.57156 0.51367 0.72671 0.87440 0.93334 0.68883 0.87677 1.37799 Bos1 0.68634 0.71150 0.68455 0.71515 0.66068 0.01971 0.00000 0.04221 0.22047 0.25129 0.28779 0.53732 0.59660 0.54889 0.63351 0.58374 0.58075 0.58141 0.56026 0.55423 0.56397 0.48976 0.71491 0.84331 0.91115 0.67433 0.85325 1.36188 A1Gallus 0.71343 0.73615 0.70955 0.73726 0.67321 0.05654 0.04221 0.00000 0.24246 0.26410 0.29790 0.53100 0.61809 0.57176 0.64066 0.59036 0.58792 0.58566 0.56948 0.55982 0.57225 0.51122 0.71178 0.85557 0.90747 0.70663 0.87218 1.36308 Manduca 0.62142 0.65570 0.62966 0.68382 0.70424 0.23445 0.22047 0.24246 0.00000 0.17951 0.32757 0.52244 0.55966 0.52216 0.63193 0.57332 0.57918 0.56703 0.55730 0.56418 0.56473 0.54676 0.76228 0.78680 0.82701 0.64552 0.80466 1.29200 Drosophila 0.73849 0.74352 0.74121 0.77994 0.74260 0.26788 0.25129 0.26410 0.17951 0.00000 0.35313 0.58016 0.63513 0.60694 0.74559 0.64294 0.64792 0.63193 0.64052 0.62925 0.63456 0.61548 0.80099 0.85231 0.94129 0.68935 0.87379 1.44483 Ascidia 0.72110 0.72883 0.68418 0.68584 0.67221 0.29607 0.28779 0.29790 0.32757 0.35313 0.00000 0.58461 0.59293 0.55242 0.66918 0.61053 0.62612 0.62934 0.62863 0.62127 0.60885 0.56783 0.74081 0.80614 0.89052 0.71498 0.90100 1.43903 Dictyostel 0.77833 0.74941 0.81793 0.80959 0.76926 0.55528 0.53732 0.53100 0.52244 0.58016 0.58461 0.00000 0.65893 0.61416 0.73849 0.65845 0.65603 0.64519 0.64110 0.63726 0.65993 0.54727 0.69075 0.82658 0.82694 0.64883 0.91374 1.31809 1Acetabula 0.82253 0.79223 0.81489 0.83779 0.78047 0.59876 0.59660 0.61809 0.55966 0.63513 0.59293 0.65893 0.00000 0.05098 0.38060 0.38575 0.38945 0.37478 0.39659 0.39917 0.39594 0.49823 0.70042 0.90364 0.83952 0.70805 0.98300 1.30473 2Acetabula 0.79457 0.77592 0.79621 0.79725 0.74114 0.55274 0.54889 0.57176 0.52216 0.60694 0.55242 0.61416 0.05098 0.00000 0.35389 0.39342 0.39257 0.37561 0.39538 0.37771 0.38359 0.47532 0.64013 0.84001 0.79305 0.65917 0.93351 1.24226 Scherffeli 0.94358 0.91096 0.94377 0.91580 0.87674 0.65111 0.63351 0.64066 0.63193 0.74559 0.66918 0.73849 0.38060 0.35389 0.00000 0.46055 0.45978 0.45702 0.44185 0.44954 0.47349 0.54496 0.76203 0.96940 0.89912 0.74821 0.97753 1.33546 Daucus 0.89250 0.86258 0.92101 0.82748 0.88585 0.58300 0.58374 0.59036 0.57332 0.64294 0.61053 0.65845 0.38575 0.39342 0.46055 0.00000 0.03130 0.06447 0.05177 0.04658 0.07001 0.47651 0.70895 0.89777 0.86890 0.71032 0.91219 1.30644 Brassica 0.88331 0.84538 0.91381 0.83948 0.89229 0.58320 0.58075 0.58792 0.57918 0.64792 0.62612 0.65603 0.38945 0.39257 0.45978 0.03130 0.00000 0.03956 0.06261 0.06159 0.08523 0.46416 0.70957 0.88176 0.86747 0.71823 0.90913 1.34332 Arabidopsi 0.88835 0.86915 0.91891 0.84573 0.89482 0.59115 0.58141 0.58566 0.56703 0.63193 0.62934 0.64519 0.37478 0.37561 0.45702 0.06447 0.03956 0.00000 0.07821 0.07026 0.11028 0.48003 0.68398 0.86310 0.85193 0.71794 0.91401 1.33718 Vigna 0.88264 0.85764 0.90629 0.83142 0.87396 0.55991 0.56026 0.56948 0.55730 0.64052 0.62863 0.64110 0.39659 0.39538 0.44185 0.05177 0.06261 0.07821 0.00000 0.05446 0.08464 0.47034 0.70452 0.88047 0.87037 0.72510 0.91658 1.33375 Gossypium 0.88588 0.86794 0.92315 0.82926 0.88187 0.56018 0.55423 0.55982 0.56418 0.62925 0.62127 0.63726 0.39917 0.37771 0.44954 0.04658 0.06159 0.07026 0.05446 0.00000 0.07539 0.48025 0.68785 0.87212 0.84491 0.72786 0.89708 1.28597 Beta 0.89461 0.88573 0.90336 0.85440 0.88986 0.57156 0.56397 0.57225 0.56473 0.63456 0.60885 0.65993 0.39594 0.38359 0.47349 0.07001 0.08523 0.11028 0.08464 0.07539 0.00000 0.47391 0.67882 0.88627 0.86914 0.74995 0.92444 1.30828 Cyanidium 0.76842 0.76555 0.75875 0.74304 0.73100 0.51367 0.48976 0.51122 0.54676 0.61548 0.56783 0.54727 0.49823 0.47532 0.54496 0.47651 0.46416 0.48003 0.47034 0.48025 0.47391 0.00000 0.65315 0.78792 0.82067 0.64642 0.84241 1.19151 Trypanosom 0.95751 0.94768 0.92906 0.88808 0.82803 0.72671 0.71491 0.71178 0.76228 0.80099 0.74081 0.69075 0.70042 0.64013 0.76203 0.70895 0.70957 0.68398 0.70452 0.68785 0.67882 0.65315 0.00000 0.83380 0.85541 0.74541 1.07920 1.40492 Trichomona 0.97047 0.97385 0.92264 0.97142 0.91662 0.87440 0.84331 0.85557 0.78680 0.85231 0.80614 0.82658 0.90364 0.84001 0.96940 0.89777 0.88176 0.86310 0.88047 0.87212 0.88627 0.78792 0.83380 0.00000 1.04712 0.83267 1.15735 1.43040 Plasmodium 1.09169 1.10571 1.08629 1.07737 1.03069 0.93334 0.91115 0.90747 0.82701 0.94129 0.89052 0.82694 0.83952 0.79305 0.89912 0.86890 0.86747 0.85193 0.87037 0.84491 0.86914 0.82067 0.85541 1.04712 0.00000 0.87348 1.23766 1.38372 Entamoeba 0.82385 0.84098 0.80406 0.83637 0.80360 0.68883 0.67433 0.70663 0.64552 0.68935 0.71498 0.64883 0.70805 0.65917 0.74821 0.71032 0.71823 0.71794 0.72510 0.72786 0.74995 0.64642 0.74541 0.83267 0.87348 0.00000 0.94897 1.33519 Nosema 0.99785 0.97982 0.95609 0.90467 0.98500 0.87677 0.85325 0.87218 0.80466 0.87379 0.90100 0.91374 0.98300 0.93351 0.97753 0.91219 0.90913 0.91401 0.91658 0.89708 0.92444 0.84241 1.07920 1.15735 1.23766 0.94897 0.00000 1.53983 Giardia 1.44940 1.47369 1.49698 1.48151 1.43601 1.37799 1.36188 1.36308 1.29200 1.44483 1.43903 1.31809 1.30473 1.24226 1.33546 1.30644 1.34332 1.33718 1.33375 1.28597 1.30828 1.19151 1.40492 1.43040 1.38372 1.33519 1.53983 0.00000 Average distance (over all possible pairs of sequences): 0.72178 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 0.06111 0.01192 29 0.03591 0.01209 Saccharomy 2 0.06422 0.01217 30 0.16441 0.02774 Candida 3 0.05999 0.01356 31 0.14262 0.02850 Neurospora 4 0.28431 0.03502 32 0.09994 0.02779 Schizosacc 5 0.30647 0.03660 33 0.11694 0.02766 Homo1 6 0.01759 0.00563 34 0.10261 0.01697 Bos1 7 0.00307 0.00254 35 0.07884 0.01586 A1Gallus 8 0.04141 0.00876 36 0.12784 0.02485 Manduca 9 0.07872 0.01486 37 0.07030 0.02193 Drosophila 10 0.11812 0.01768 38 0.06822 0.02043 Ascidia 11 0.21429 0.02474 39 0.14734 0.02393 Dictyostel 12 0.34440 0.03782 40 0.09207 0.02238 1Acetabula 13 0.04551 0.00993 41 0.02915 0.00889 2Acetabula 14 0.00927 0.00594 42 0.02893 0.00909 Scherffeli 15 0.24508 0.03012 43 0.16485 0.02564 Daucus 16 0.02668 0.00789 44 0.10984 0.02437 Brassica 17 0.01039 0.00608 45 0.06964 0.02161 Arabidopsi 18 0.04176 0.00956 46 0.07722 0.02386 Vigna 19 0.03222 0.00834 Gossypium 20 0.02984 0.00808 Beta 21 0.03425 0.00956 Cyanidium 22 0.28595 0.03531 Trypanosom 23 0.47385 0.04863 Trichomona 24 0.60224 0.05809 Plasmodium 25 0.65906 0.06175 Entamoeba 26 0.46975 0.04860 Nosema 27 0.67528 0.06394 18 iterations until convergence Giardia 28 1.30156 0.11797 log L: -15067.83 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Giardia:1.30156,Trypanosom:0.47385,Trichomona:0.60224,Plasmodium:0.65906, Entamoeba:0.46975,((Dictyostel:0.34440,((Nosema:0.67528,(Schizosacc:0.30647, (Neurospora:0.28431,(Candida:0.05999,(Eremotheci:0.06111,Saccharomy:0.06422) :0.03591):0.16441):0.14262):0.09994):0.11694,(Ascidia:0.21429,(Homo1:0.01759, Bos1:0.00307,A1Gallus:0.04141):0.10261,(Manduca:0.07872,Drosophila:0.11812) :0.07884):0.12784):0.07030):0.06822,(Cyanidium:0.28595,((Scherffeli:0.24508, (1Acetabula:0.04551,2Acetabula:0.00927):0.14734):0.09207,(Beta:0.03425, (Vigna:0.03222,Gossypium:0.02984,(Daucus:0.02668,Brassica:0.01039, Arabidopsi:0.04176):0.02915):0.02893):0.16485):0.10984):0.06964):0.07722); TIME STAMP Date and time: Wed Mar 15 12:28:00 2000 Runtime: 546 seconds (= 9.1 minutes = 0.2 hours)