#NEXUS Begin trees; [Treefile saved Wed Oct 20 14:44:54 2004] [! >Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r3.0/At4g22670.1.cds.nex >Branch-and-bound search settings: > Optimality criterion = likelihood > Likelihood settings: > User-specified substitution rate matrix = > - 1.000000 1.571600 1.000000 > 1.000000 - 1.000000 3.573100 > 1.571600 1.000000 - 1.000000 > 1.000000 3.573100 1.000000 - > Assumed nucleotide frequencies (set by user): > A=0.31230 C=0.19520 G=0.27110 T=0.22140 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 0.9023 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the GTR+G model > Number of distinct data patterns under this model = 143 > 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 > Initial upper bound: unknown (compute heuristically) > Addition sequence: as-is > 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 > >Branch-and-bound search completed: > Score of best tree found = 3269.35260 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.18 sec) ] Translate 1 lgn_214772, 2 stgn_175368, 3 cangn_196448, 4 cgn_119680, 5 At4g22670.1 ; tree PAUP_1 = [&R] ((((1:0.024280,2:0.036750):0.014028,3:0.091578):0.114446,4:0.137983):0.321899,5:0); End;