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: 13 sequences with 561 amino acid sites Number of constant sites: 6 (= 1.1% of all sites) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 10.6% pi(R) = 6.6% pi(N) = 2.6% pi(D) = 5.9% pi(C) = 1.4% pi(Q) = 2.3% pi(E) = 6.8% pi(G) = 7.7% pi(H) = 3.2% pi(I) = 4.7% pi(L) = 10.9% pi(K) = 3.7% pi(M) = 2.1% pi(F) = 4.1% pi(P) = 5.5% pi(S) = 5.7% pi(T) = 4.7% pi(W) = 1.3% pi(Y) = 2.8% pi(V) = 7.5% RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value Mycobacter failed 2.50% [1] Mycobacte2 passed 12.37% [5] Streptomyc failed 0.00% [8] Lysobacter failed 0.00% [8] Deinococcu failed 1.85% [5] Streptomy2 failed 0.00% [3] Rattusnorv failed 0.92% [2] Rattusnor2 failed 0.55% [2] Homosapien failed 0.00% [3] Celegans failed 1.65% [3] Saccharomy failed 0.67% [2] Aeropyrum passed 16.15% [14] Bacillus failed 1.82% [16] 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 18 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. 13 Mycobacter 0.00000 0.15926 2.15166 2.09829 2.58381 2.62545 3.42614 3.42655 3.56139 3.29863 3.01954 2.71485 2.15562 Mycobacte2 0.15926 0.00000 2.27634 2.18391 2.54287 2.57995 3.27532 3.28563 3.29245 3.20338 3.09874 2.74326 2.25381 Streptomyc 2.15166 2.27634 0.00000 0.66492 2.44625 2.51308 3.11485 3.11405 3.13171 3.29703 3.08112 2.36331 2.51456 Lysobacter 2.09829 2.18391 0.66492 0.00000 2.80088 2.55386 3.23355 3.23264 3.25789 3.45544 3.26507 2.56001 2.45368 Deinococcu 2.58381 2.54287 2.44625 2.80088 0.00000 0.79835 1.89542 1.89802 1.86786 1.91080 1.70740 2.60998 2.54303 Streptomy2 2.62545 2.57995 2.51308 2.55386 0.79835 0.00000 1.69767 1.70085 1.73859 1.88199 1.77764 2.60981 2.49724 Rattusnorv 3.42614 3.27532 3.11485 3.23355 1.89542 1.69767 0.00000 0.00652 0.16632 0.85741 1.06962 2.76796 2.91232 Rattusnor2 3.42655 3.28563 3.11405 3.23264 1.89802 1.70085 0.00652 0.00000 0.17056 0.85932 1.07075 2.76843 2.90718 Homosapien 3.56139 3.29245 3.13171 3.25789 1.86786 1.73859 0.16632 0.17056 0.00000 0.87059 1.02950 2.85839 2.85641 Celegans 3.29863 3.20338 3.29703 3.45544 1.91080 1.88199 0.85741 0.85932 0.87059 0.00000 1.13706 2.97547 2.93868 Saccharomy 3.01954 3.09874 3.08112 3.26507 1.70740 1.77764 1.06962 1.07075 1.02950 1.13706 0.00000 2.85072 2.77019 Aeropyrum 2.71485 2.74326 2.36331 2.56001 2.60998 2.60981 2.76796 2.76843 2.85839 2.97547 2.85072 0.00000 2.22336 Bacillus 2.15562 2.25381 2.51456 2.45368 2.54303 2.49724 2.91232 2.90718 2.85641 2.93868 2.77019 2.22336 0.00000 Average distance (over all possible pairs of sequences): 2.33605 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: 715 Unresolved quartets: 18 (= 2.5%) 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. :---Streptomyc :------------------------100: : :---Lysobacter : : :---Rattusnorv : :100: : :100: :---Rattusnor2 : : : : :100: :-------Homosapien :100: : : : : :100: :-----------Celegans : : : : : : :100: :---------------Saccharomy : : : : : : : : :---Deinococcu : : :-75: :-------------99: : : : : :---Streptomy2 : :-95: : : : :-----------------------Aeropyrum : : : :---------------------------Bacillus : :-----------------------------------Mycobacte2 : :-----------------------------------Mycobacter Quartet puzzling tree (in CLUSTAL W notation): (Mycobacter,((Streptomyc,Lysobacter)100,(((((((Rattusnorv,Rattusnor2)100, Homosapien)100,Celegans)100,Saccharomy)100,(Deinococcu,Streptomy2)99)100, Aeropyrum)75,Bacillus)95)100,Mycobacte2); 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) **..****** *** : 1000 **........ ... : 1000 ******.... *** : 1000 ****...... .** : 1000 ******..** *** : 1000 ******...* *** : 1000 ******.... .** : 1000 ****..**** *** : 994 ****...... ... : 953 ****...... ..* : 749 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ********** *.. : 196 ****...... .*. : 54 **........ ..* : 26 **..****** *.. : 7 **........ .** : 6 *****..... .** : 6 **..****** **. : 5 **..****** *.* : 3 **........ .*. : 1 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---3 Streptomyc :------14 : :---4 Lysobacter :--------23 : : :-7 Rattusnorv : : :-15 : : : :-8 Rattusnor2 : : :---16 : : : :-9 Homosapien : : :--17 : : : :----10 Celegans : : :------18 : : : :----11 Saccharomy : : :-----20 : : : : :---5 Deinococcu : : : :---19 : : : :----6 Streptomy2 : : :-21 : : : :---------12 Aeropyrum : :--22 : :---------13 Bacillus : :-2 Mycobacte2 : :-1 Mycobacter branch length S.E. branch length S.E. Mycobacter 1 0.03954 0.01816 14 0.78433 0.10127 Mycobacte2 2 0.11973 0.02033 15 0.08420 0.01775 Streptomyc 3 0.28195 0.04624 16 0.35399 0.04361 Lysobacter 4 0.38258 0.04947 17 0.20594 0.04799 Deinococcu 5 0.39848 0.05259 18 0.67304 0.08329 Streptomy2 6 0.42345 0.05358 19 0.31697 0.06892 Rattusnorv 7 0.00099 0.00228 20 0.64763 0.09974 Rattusnor2 8 0.00553 0.00367 21 0.03558 0.07636 Homosapien 9 0.08339 0.01760 22 0.24972 0.08107 Celegans 10 0.45634 0.04768 23 1.00409 0.10838 Saccharomy 11 0.49241 0.05601 Aeropyrum 12 1.19018 0.11805 20 iterations until convergence Bacillus 13 1.09518 0.11289 log L: -10628.34 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Mycobacter:0.03954,((Streptomyc:0.28195,Lysobacter:0.38258)100:0.78433, (((((((Rattusnorv:0.00099,Rattusnor2:0.00553)100:0.08420,Homosapien:0.08339) 100:0.35399,Celegans:0.45634)100:0.20594,Saccharomy:0.49241)100:0.67304, (Deinococcu:0.39848,Streptomy2:0.42345)99:0.31697)100:0.64763,Aeropyrum:1.19018) 75:0.03558,Bacillus:1.09518)95:0.24972)100:1.00409,Mycobacte2:0.11973); TIME STAMP Date and time: Thu Dec 02 21:22:05 1999 Runtime: 269 seconds (= 4.5 minutes = 0.1 hours)