#NEXUS Begin trees; [Treefile saved Wed Oct 20 16:23:58 2004] [! >Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At1g10500.1.cds.nex >Branch-and-bound search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio = 2.2808 (kappa = 4.5616) > Assumed nucleotide frequencies (set by user): > A=0.25000 C=0.25000 G=0.25000 T=0.25000 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 0.2105 > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the K80(K2P)+G model > Number of distinct data patterns under this model = 16 > 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) = 387.84464 > 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 = 435.93299 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.07 sec) ] Translate 1 lgn_145260, 2 stgn_192738, 3 cangn_197791, 4 cgn_125354, 5 At1g10500.1 ; tree PAUP_1 = [&R] (((1:0,2:0.006319):0.020729,(3:2.538e-08,4:0.194653):0.028110):0.416855,5:0); End;