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: 12 sequences with 1983 nucleotide sites Number of constant sites: 50 (= 2.5% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.13 (S.E. 0.06) Nucleotide frequencies (estimated from data set): pi(A) = 28.7% pi(C) = 21.8% pi(G) = 25.0% pi(T) = 24.5% Expected transition/transversion ratio: 1.14 Expected pyrimidine transition/purine transition ratio: 0.74 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value PIG failed 0.01% [22] COW failed 0.03% [21] FLY failed 0.00% [16] CELEGANS passed 63.30% [8] FLOWER failed 0.73% [1] SOY failed 0.10% [22] HOMO failed 3.19% [25] MOUSE passed 35.99% [13] RAT passed 27.46% [11] FROG failed 2.04% [13] TROUT failed 3.11% [16] DANIO passed 44.15% [12] The chi-square tests compares the nucleotide 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 45 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. 12 PIG 0.00000 0.07191 0.91436 0.94461 0.85391 0.87144 0.71588 0.68665 0.68646 0.78026 0.76103 0.81780 COW 0.07191 0.00000 0.88027 0.90082 0.81596 0.83184 0.67543 0.62680 0.64141 0.75925 0.73627 0.77553 FLY 0.91436 0.88027 0.00000 0.35217 0.46267 0.39674 0.36875 0.35734 0.33146 0.37050 0.28117 0.32063 CELEGANS 0.94461 0.90082 0.35217 0.00000 0.39146 0.35211 0.34575 0.35490 0.36315 0.34653 0.37989 0.39307 FLOWER 0.85391 0.81596 0.46267 0.39146 0.00000 0.18093 0.46986 0.43746 0.42701 0.43842 0.39115 0.42353 SOY 0.87144 0.83184 0.39674 0.35211 0.18093 0.00000 0.30099 0.30252 0.31390 0.31828 0.36048 0.33943 HOMO 0.71588 0.67543 0.36875 0.34575 0.46986 0.30099 0.00000 0.14364 0.13530 0.23502 0.22124 0.26654 MOUSE 0.68665 0.62680 0.35734 0.35490 0.43746 0.30252 0.14364 0.00000 0.06541 0.25600 0.22066 0.27112 RAT 0.68646 0.64141 0.33146 0.36315 0.42701 0.31390 0.13530 0.06541 0.00000 0.23709 0.21685 0.25228 FROG 0.78026 0.75925 0.37050 0.34653 0.43842 0.31828 0.23502 0.25600 0.23709 0.00000 0.21425 0.26379 TROUT 0.76103 0.73627 0.28117 0.37989 0.39115 0.36048 0.22124 0.22066 0.21685 0.21425 0.00000 0.17847 DANIO 0.81780 0.77553 0.32063 0.39307 0.42353 0.33943 0.26654 0.27112 0.25228 0.26379 0.17847 0.00000 Average distance (over all possible pairs of sequences): 0.45148 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: 495 Unresolved quartets: 45 (= 9.1%) 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 not completely resolved! :---TROUT :-----75: : :---DANIO : : :---FLOWER : :-99: :-83: : :---SOY : :-63: : : : :---FLY : : :-59: : : :---CELEGANS :100: : : : :-----------FROG : : : : :---MOUSE : : :-91: : :-----63: :---RAT : : : :-------HOMO : :-------------------COW : :-------------------PIG Quartet puzzling tree (in CLUSTAL W notation): (PIG,(((TROUT,DANIO)75,((FLOWER,SOY)99,(FLY,CELEGANS)59)63, FROG)83,((MOUSE,RAT)91,HOMO)63)100,COW); 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) **........ .. : 998 ****..**** ** : 989 *******..* ** : 906 **....***. .. : 834 ********** .. : 750 **....**** ** : 634 ******...* ** : 627 **..****** ** : 590 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *********. .. : 474 ***...**** ** : 351 **....**** .. : 320 **.....**. .. : 285 *********. .* : 176 **..****** .. : 171 **..*****. .. : 153 **.******* .. : 95 **....*... .. : 69 ******.... .. : 61 **.******. .. : 55 **....***. ** : 54 ******.*.* ** : 43 ******.... ** : 43 ******..** ** : 42 ****..***. ** : 32 **..**.... .. : 30 **....**** *. : 28 **..****** *. : 24 ******.**. ** : 17 (41 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. :---11 TROUT :--13 : :----12 DANIO :--17 : : :----5 FLOWER : : :-----14 : : : :--6 SOY : :---16 : : : :------3 FLY : : :--15 : : :------4 CELEGANS : : : :----10 FROG :--------------20 : : :--8 MOUSE : : :--18 : : : :-9 RAT : :--19 : :--7 HOMO : :-2 COW : :--1 PIG branch length S.E. branch length S.E. PIG 1 0.05378 0.01042 13 0.07028 0.01254 COW 2 0.01776 0.00800 14 0.16655 0.01645 FLY 3 0.18975 0.01523 15 0.04675 0.01054 CELEGANS 4 0.18615 0.01561 16 0.09490 0.01232 FLOWER 5 0.12425 0.01453 17 0.04422 0.01002 SOY 6 0.06858 0.01434 18 0.04915 0.00736 HOMO 7 0.06987 0.00832 19 0.04488 0.00964 MOUSE 8 0.03739 0.00582 20 0.47169 0.03787 RAT 9 0.03036 0.00532 FROG 10 0.13051 0.01165 TROUT 11 0.07658 0.01285 19 iterations until convergence DANIO 12 0.11480 0.01433 log L: -10774.21 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (PIG:0.05378,(((TROUT:0.07658,DANIO:0.11480)75:0.07028,((FLOWER:0.12425, SOY:0.06858)99:0.16655,(FLY:0.18975,CELEGANS:0.18615)59:0.04675) 63:0.09490,FROG:0.13051)83:0.04422,((MOUSE:0.03739,RAT:0.03036)91:0.04915, HOMO:0.06987)63:0.04488)100:0.47169,COW:0.01776); TIME STAMP Date and time: Wed Jun 04 20:29:51 2003 Runtime: 11 seconds (= 0.2 minutes = 0.0 hours)