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 7529 nucleotide sites Number of constant sites: 6 (= 0.1% 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) = 33.7% pi(C) = 18.6% pi(G) = 24.9% pi(T) = 22.8% Expected transition/transversion ratio: 1.10 Expected pyrimidine transition/purine transition ratio: 0.51 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value FLY failed 0.00% [1] CELEGANS passed 29.21% [0] FLOWER failed 0.18% [0] SOY passed 5.10% [0] FROG failed 0.43% [1] TROUT failed 0.05% [1] DANIO failed 0.00% [1] PIG failed 0.00% [0] HOMO failed 0.00% [0] COW failed 0.00% [0] MOUSE failed 1.88% [0] RAT passed 86.04% [0] 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 1 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 FLY 0.00000 0.52746 0.57031 0.47533 0.56325 0.48144 0.56385 0.95828 0.58071 0.55540 0.56066 0.57047 CELEGANS 0.52746 0.00000 0.48523 0.54938 0.56402 0.43758 0.56889 1.04668 0.51893 0.52467 0.51630 0.50776 FLOWER 0.57031 0.48523 0.00000 0.28153 0.60174 0.57516 0.65879 1.36522 0.57826 0.56847 0.58528 0.59136 SOY 0.47533 0.54938 0.28153 0.00000 0.48128 0.61150 0.59225 1.79520 0.56262 0.53224 0.52690 0.54885 FROG 0.56325 0.56402 0.60174 0.48128 0.00000 0.17877 0.25018 0.57916 0.22960 0.23267 0.23761 0.22852 TROUT 0.48144 0.43758 0.57516 0.61150 0.17877 0.00000 0.17510 0.74924 0.28685 0.26462 0.27227 0.27958 DANIO 0.56385 0.56889 0.65879 0.59225 0.25018 0.17510 0.00000 0.62897 0.29819 0.27859 0.28448 0.27837 PIG 0.95828 1.04668 1.36522 1.79520 0.57916 0.74924 0.62897 0.00000 0.37940 0.36695 0.42060 0.38854 HOMO 0.58071 0.51893 0.57826 0.56262 0.22960 0.28685 0.29819 0.37940 0.00000 0.05492 0.11474 0.12763 COW 0.55540 0.52467 0.56847 0.53224 0.23267 0.26462 0.27859 0.36695 0.05492 0.00000 0.11392 0.12295 MOUSE 0.56066 0.51630 0.58528 0.52690 0.23761 0.27227 0.28448 0.42060 0.11474 0.11392 0.00000 0.08300 RAT 0.57047 0.50776 0.59136 0.54885 0.22852 0.27958 0.27837 0.38854 0.12763 0.12295 0.08300 0.00000 Average distance (over all possible pairs of sequences): 0.47710 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: 1 (= 0.2%) 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! :---MOUSE :-96: : :---RAT :-76: : : :---HOMO :-98: :-96: : : :---COW : : : :-----------PIG :100: : : :---TROUT : :---------72: : : :---DANIO : : : :---------------FROG : : :---FLOWER : :100: :---------75: :---SOY : : : :-------CELEGANS : :-------------------FLY Quartet puzzling tree (in CLUSTAL W notation): (FLY,((((MOUSE,RAT)96,(HOMO,COW)96)76,PIG)98,(TROUT,DANIO)72, FROG)100,((FLOWER,SOY)100,CELEGANS)75); 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 *******... .. : 982 ********** .. : 963 ********.. ** : 957 ********.. .. : 763 *...****** ** : 748 *****..*** ** : 721 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****...*** ** : 497 ****.**... .. : 387 ****.*.*** ** : 256 *.**...... .. : 229 *******... ** : 167 *****..... .. : 71 ****.*.... .. : 58 *******.** .. : 54 *******.*. ** : 40 **........ .. : 23 *******... *. : 19 ****.***.. .. : 14 *******.** *. : 9 *******.** .* : 8 ********.. *. : 7 ****...*.. .. : 4 ****.***** .. : 4 ********.* .. : 4 ****..*... .. : 3 ****..**** ** : 3 (6 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 MOUSE :-13 : :-12 RAT :-15 : : :-9 HOMO : :-14 : :-10 COW :--16 : :-----8 PIG :----18 : : :--6 TROUT : :-17 : : :--7 DANIO : : : :--5 FROG : : :--3 FLOWER : :---19 : : :---4 SOY :-20 : :----2 CELEGANS : :----1 FLY branch length S.E. branch length S.E. FLY 1 0.25803 0.01357 13 0.01729 0.00314 CELEGANS 2 0.22269 0.01368 14 0.04683 0.00423 FLOWER 3 0.12379 0.01267 15 0.00001 0.00019 SOY 4 0.14285 0.02189 16 0.09446 0.00647 FROG 5 0.12241 0.00707 17 0.05653 0.00758 TROUT 6 0.08242 0.01561 18 0.23106 0.01398 DANIO 7 0.11479 0.00776 19 0.14338 0.01348 PIG 8 0.33149 0.03121 20 0.04402 0.01128 HOMO 9 0.02371 0.00296 COW 10 0.03468 0.00335 MOUSE 11 0.02722 0.00375 23 iterations until convergence RAT 12 0.04677 0.00392 log L: -28378.25 WARNING --- at least one brach length is close to an internal boundary! Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (FLY:0.25803,((((MOUSE:0.02722,RAT:0.04677)96:0.01729,(HOMO:0.02371, COW:0.03468)96:0.04683)76:0.00001,PIG:0.33149)98:0.09446,(TROUT:0.08242, DANIO:0.11479)72:0.05653,FROG:0.12241)100:0.23106,((FLOWER:0.12379, SOY:0.14285)100:0.14338,CELEGANS:0.22269)75:0.04402); TIME STAMP Date and time: Wed Jun 04 20:19:49 2003 Runtime: 27 seconds (= 0.5 minutes = 0.0 hours)