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 5229 nucleotide sites Number of constant sites: 0 (= 0.0% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.05 (S.E. 0.03) Nucleotide frequencies (estimated from data set): pi(A) = 25.6% pi(C) = 24.6% pi(G) = 27.3% pi(T) = 22.5% Expected transition/transversion ratio: 1.06 Expected pyrimidine transition/purine transition ratio: 0.80 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value FLOWER failed 0.00% [2] SOY failed 0.11% [1] FLY passed 66.60% [5] CELEGANS passed 9.14% [4] FROG failed 0.00% [2] TROUT failed 2.88% [6] DANIO passed 66.72% [3] MOUSE failed 0.06% [2] RAT failed 0.00% [0] HOMO failed 0.00% [1] PIG failed 0.56% [5] COW failed 0.00% [5] 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 9 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 FLOWER 0.00000 0.19603 0.66495 0.63115 0.55045 0.48383 0.60136 0.56139 0.57392 0.59437 0.51030 0.60373 SOY 0.19603 0.00000 0.47330 0.49296 0.38795 0.40848 0.41198 0.42176 0.39994 0.41287 0.44711 1.73305 FLY 0.66495 0.47330 0.00000 0.41554 0.50582 0.42557 0.50154 0.48217 0.49187 0.49573 0.40878 0.47266 CELEGANS 0.63115 0.49296 0.41554 0.00000 0.54327 0.49710 0.54189 0.52968 0.55162 0.57009 0.53565 0.58508 FROG 0.55045 0.38795 0.50582 0.54327 0.00000 0.28626 0.30953 0.32639 0.28350 0.34124 0.28025 0.28568 TROUT 0.48383 0.40848 0.42557 0.49710 0.28626 0.00000 0.21444 0.24981 0.24670 0.24558 0.23977 0.56979 DANIO 0.60136 0.41198 0.50154 0.54189 0.30953 0.21444 0.00000 0.32018 0.29367 0.31812 0.26426 0.26488 MOUSE 0.56139 0.42176 0.48217 0.52968 0.32639 0.24981 0.32018 0.00000 0.06207 0.19493 0.11402 0.14627 RAT 0.57392 0.39994 0.49187 0.55162 0.28350 0.24670 0.29367 0.06207 0.00000 0.15268 0.12232 0.15005 HOMO 0.59437 0.41287 0.49573 0.57009 0.34124 0.24558 0.31812 0.19493 0.15268 0.00000 0.08564 0.13040 PIG 0.51030 0.44711 0.40878 0.53565 0.28025 0.23977 0.26426 0.11402 0.12232 0.08564 0.00000 0.08218 COW 0.60373 1.73305 0.47266 0.58508 0.28568 0.56979 0.26488 0.14627 0.15005 0.13040 0.08218 0.00000 Average distance (over all possible pairs of sequences): 0.40448 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: 9 (= 1.8%) 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! :---FLY :------------100: : :---CELEGANS : : :---MOUSE : :100: : : :---RAT :100: :100: : : : : :---HOMO : : : : : : : : :-83:---PIG : : :-81: : : : : : :---COW : : : : : :-97: : :---TROUT : : :-----94: : : :---DANIO : : : :---------------FROG : :-----------------------SOY : :-----------------------FLOWER Quartet puzzling tree (in CLUSTAL W notation): (FLOWER,((FLY,CELEGANS)100,((((MOUSE,RAT)100,(HOMO,PIG,COW)83)100, (TROUT,DANIO)94)81,FROG)97)100,SOY); 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 *******... .. : 999 **........ .. : 997 **..****** ** : 995 ****...... .. : 966 *****..*** ** : 936 *********. .. : 828 *****..... .. : 807 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ********** .. : 474 *********. .* : 359 *********. *. : 161 ****...*** ** : 106 *******... ** : 96 ****.**... .. : 80 *******... *. : 29 ******.... .. : 28 *******... .* : 17 *******..* *. : 17 *****.*... .. : 17 ****.*.*** ** : 15 *******..* .* : 11 **..*..... .. : 10 **...**... .. : 10 **..***... .. : 9 *******..* .. : 8 ****.*.... .. : 4 **.*...... .. : 4 **..*..*** ** : 3 (8 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. :---3 FLY :--13 : :----4 CELEGANS :----20 : : :-8 MOUSE : : :--14 : : : :-9 RAT : : :--16 : : : : :--10 HOMO : : : :-15 : : : :-11 PIG : : : : : : : :-12 COW : : :-18 : : : : :--6 TROUT : : : :-17 : : : :--7 DANIO : :--19 : :---5 FROG : :--2 SOY : :---1 FLOWER branch length S.E. branch length S.E. FLOWER 1 0.14290 0.01464 13 0.12457 0.01214 SOY 2 0.07761 0.01685 14 0.06788 0.00615 FLY 3 0.18387 0.01252 15 0.02333 0.00613 CELEGANS 4 0.23306 0.01535 16 0.08588 0.00740 FROG 5 0.16005 0.00950 17 0.05763 0.00828 TROUT 6 0.09744 0.01361 18 0.03447 0.00646 DANIO 7 0.12308 0.00920 19 0.08616 0.01041 MOUSE 8 0.03902 0.00451 20 0.24103 0.01655 RAT 9 0.03148 0.00392 HOMO 10 0.08605 0.00686 PIG 11 0.02058 0.00738 14 iterations until convergence COW 12 0.06330 0.01174 log L: -23328.15 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (FLOWER:0.14290,((FLY:0.18387,CELEGANS:0.23306)100:0.12457,((((MOUSE:0.03902, RAT:0.03148)100:0.06788,(HOMO:0.08605,PIG:0.02058,COW:0.06330)83:0.02333) 100:0.08588,(TROUT:0.09744,DANIO:0.12308)94:0.05763)81:0.03447,FROG:0.16005) 97:0.08616)100:0.24103,SOY:0.07761); TIME STAMP Date and time: Wed Jun 04 20:21:20 2003 Runtime: 23 seconds (= 0.4 minutes = 0.0 hours)