P A U P * Portable version 4.0b10 for Unix Fri Jun 2 02:35:57 2006 -----------------------------NOTICE----------------------------- This is a beta-test version. Please report any crashes, apparent calculation errors, or other anomalous results. There are no restrictions on publication of results obtained with this version, but you should check the WWW site frequently for bug announcements and/or updated versions. See the README file on the distribution media for details. ---------------------------------------------------------------- Processing of file "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2491.fasta" begins... Warning: Use of all-digit taxon and/or character names does not conform to the NEXUS standard and is strongly discouraged. Remember that names have priority over numbers. Data read in DNA format Data matrix has 7 taxa, 312 characters Valid character-state symbols: ACGT Missing data identified by '?' Gaps identified by '-' "Equate" macros in effect: R,r ==> {AG} Y,y ==> {CT} M,m ==> {AC} K,k ==> {GT} S,s ==> {CG} W,w ==> {AT} H,h ==> {ACT} B,b ==> {CGT} V,v ==> {ACG} D,d ==> {AGT} N,n ==> {ACGT} Processing of file "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2491.fasta" completed. Optimality criterion set to likelihood. Heuristic search settings: Optimality criterion = likelihood Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio = 1.1395 (kappa = 2.3632248) Assumed nucleotide frequencies (set by user): A=0.32850 C=0.18770 G=0.20690 T=0.27690 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = 1.4745 Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 156 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Starting tree(s) obtained via stepwise addition Addition sequence: random Number of replicates = 10 Starting seed = 703031741 Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 Branches collapsed (creating polytomies) if branch length is less than or equal to 1e-08 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Heuristic search completed Total number of rearrangements tried = 313 Score of best tree(s) found = 1712.01394 Number of trees retained = 1 Time used = 8 sec (CPU time = 7.86 sec) Tree-island profile: First Last First Times Island Size tree tree Score replicate hit ---------------------------------------------------------------------- 1 1 1 1 1712.01394 1 10 Tree description: Unrooted tree(s) rooted using outgroup method Optimality criterion = likelihood Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio = 1.1395 (kappa = 2.3632248) Assumed nucleotide frequencies (set by user): A=0.32850 C=0.18770 G=0.20690 T=0.27690 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = 1.4745 Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 156 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Tree number 1 (rooted using default outgroup) Branch lengths and linkages for tree #1 (unrooted) Connected Branch Standard Node to node length error --------------------------------------------------------- 113253 (1) 12 1.567e-06 0.02730 11 12 0.09709 0.02685 10 11 0.11213 0.02914 9 10 0.01891 0.01611 14666 (2) 9 0.01088 0.00676 8 9 0.00792 0.00612 81506 (5) 8 0.01410 0.00722 99987 (6) 8 0.05972 0.01497 30797 (4) 10 0.31744 0.04572 At1g26660.1 (7) 11 0.39146 0.05673 30559 (3) 12 2.66438 0.50293 --------------------------------------------------------- Sum 3.69402 -Ln likelihood = 1712.01392 / 113253 | | / 14666 | | | /9 81506 | |8 12/-10\- 99987 | | | +11 \-------- 30797 | | | \---------- At1g26660.1 | \------------------------------------------------------------------ 30559 1 tree saved to file "~/new_at_family_tcoffee/4_20/trees_4_20/2491.ml.tre"