PUZZLE 4.0.2 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: 11 sequences with 536 amino acid sites Number of constant sites: 46 (= 8.6% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 12.1% pi(R) = 6.2% pi(N) = 2.5% pi(D) = 5.1% pi(C) = 1.3% pi(Q) = 2.8% pi(E) = 6.0% pi(G) = 9.7% pi(H) = 3.0% pi(I) = 4.6% pi(L) = 10.2% pi(K) = 3.5% pi(M) = 2.4% pi(F) = 3.9% pi(P) = 5.2% pi(S) = 5.5% pi(T) = 4.2% pi(W) = 0.7% pi(Y) = 3.2% pi(V) = 7.8% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value M.tubercul failed 0.00% [5] Streptomyc failed 0.00% [4] Deinococcu failed 0.57% [6] Rhodobacte failed 0.04% [5] Pseudomona failed 2.65% [2] Salmonella passed 9.73% [5] Synechocys failed 0.00% [7] Methonobac failed 3.37% [3] Methanococ failed 0.00% [2] Archaeoglo failed 0.00% [5] Bacillus failed 0.16% [4] 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 12 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. 11 M.tubercul 0.00000 0.65067 1.05614 1.23169 1.36987 1.41826 1.46246 1.27509 1.53856 1.44707 1.48950 Streptomyc 0.65067 0.00000 0.95822 1.33045 1.30137 1.33811 1.34206 1.18655 1.44620 1.38086 1.38396 Deinococcu 1.05614 0.95822 0.00000 1.10619 1.33575 1.17069 1.31296 1.22948 1.40488 1.37094 1.25822 Rhodobacte 1.23169 1.33045 1.10619 0.00000 0.80870 1.31811 1.42561 1.45025 1.66339 1.53941 1.49485 Pseudomona 1.36987 1.30137 1.33575 0.80870 0.00000 1.64167 1.52028 1.54751 1.78168 1.48709 1.48139 Salmonella 1.41826 1.33811 1.17069 1.31811 1.64167 0.00000 1.29776 1.25275 1.48834 1.40513 1.26436 Synechocys 1.46246 1.34206 1.31296 1.42561 1.52028 1.29776 0.00000 1.42793 1.47661 1.37716 1.30948 Methonobac 1.27509 1.18655 1.22948 1.45025 1.54751 1.25275 1.42793 0.00000 0.79556 1.08714 1.25038 Methanococ 1.53856 1.44620 1.40488 1.66339 1.78168 1.48834 1.47661 0.79556 0.00000 1.13167 1.22580 Archaeoglo 1.44707 1.38086 1.37094 1.53941 1.48709 1.40513 1.37716 1.08714 1.13167 0.00000 1.32182 Bacillus 1.48950 1.38396 1.25822 1.49485 1.48139 1.26436 1.30948 1.25038 1.22580 1.32182 0.00000 Average distance (over all possible pairs of sequences): 1.32851 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: 1000 Analysed quartets: 330 Unresolved quartets: 12 (= 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 completely resolved. :---Rhodobacte :-------------99: : :---Pseudomona : : :---Methonobac :-71: :-99: : : :-98: :---Methanococ : : : : : : :-62: :-------Archaeoglo : : : : :-99: :-87: :-----------Bacillus : : : : : : :---Salmonella : : :---------50: : : :---Synechocys : : : :-----------------------Deinococcu : :---------------------------Streptomyc : :---------------------------M.tubercul Quartet puzzling tree (in CLUSTAL W notation): (M.tubercul,(((Rhodobacte,Pseudomona)99,((((Methonobac,Methanococ)99, Archaeoglo)98,Bacillus)62,(Salmonella,Synechocys)50)87)71, Deinococcu)99,Streptomyc); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps: Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **........ . : 993 *******..* * : 992 ***..***** * : 989 *******... * : 982 *****..... . : 867 ***....... . : 711 *******... . : 623 *****..*** * : 503 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ******.... . : 221 *****..*** . : 195 **.**..... . : 165 *****.*... . : 143 *****.**** . : 125 ******.*** . : 115 **...***** * : 109 ***...**** * : 40 ***....*** * : 34 ***....*** . : 31 ******.... * : 22 *****.*... * : 13 *****..... * : 11 ***..*.... . : 9 ***..*.*** * : 8 **.**.**** * : 7 **.....*** * : 7 *******..* . : 6 **....**** * : 5 ***..**... . : 5 (28 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. :------4 Rhodobacte :------12 : :--------5 Pseudomona :--18 : : :------8 Methonobac : : :---13 : : : :-------9 Methanococ : : :----14 : : : :---------10 Archaeoglo : : :---15 : : : :---------11 Bacillus : :---17 : : :----------6 Salmonella : :--16 : :-----------7 Synechocys :------19 : :------3 Deinococcu : :-----2 Streptomyc : :------1 M.tubercul branch length S.E. branch length S.E. M.tubercul 1 0.38386 0.04191 12 0.37611 0.04941 Streptomyc 2 0.28388 0.03789 13 0.19679 0.03952 Deinococcu 3 0.39293 0.04391 14 0.20647 0.04154 Rhodobacte 4 0.34669 0.04388 15 0.14987 0.03702 Pseudomona 5 0.47625 0.05066 16 0.10997 0.03685 Salmonella 6 0.64088 0.05953 17 0.15396 0.03846 Synechocys 7 0.68934 0.06202 18 0.10351 0.03363 Methonobac 8 0.38965 0.04390 19 0.34211 0.04538 Methanococ 9 0.42564 0.04576 Archaeoglo 10 0.57413 0.05504 8 iterations until convergence Bacillus 11 0.57429 0.05461 log L: -10494.14 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (M.tubercul:0.38386,(((Rhodobacte:0.34669,Pseudomona:0.47625)99:0.37611, ((((Methonobac:0.38965,Methanococ:0.42564)99:0.19679,Archaeoglo:0.57413) 98:0.20647,Bacillus:0.57429)62:0.14987,(Salmonella:0.64088,Synechocys:0.68934) 50:0.10997)87:0.15396)71:0.10351,Deinococcu:0.39293)99:0.34211,Streptomyc:0.28388); TIME STAMP Date and time: Thu Mar 30 19:47:18 2000 Runtime: 58 seconds (= 1.0 minutes = 0.0 hours)