#NEXUS Begin trees; [Treefile saved Thu Oct 21 11:03:39 2004] [! >Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At3g54360.1.cds.nex >Branch-and-bound search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio = 1.4937 (kappa = 3.0700459) > Assumed nucleotide frequencies (set by user): > A=0.28920 C=0.18980 G=0.22750 T=0.29350 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = 0.4907 > 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 = 74 > 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 = 1483.41004 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.02 sec) ] Translate 1 lgn_146279, 2 cangn_198557, 3 cgn_128234, 4 At3g54360.1 ; tree PAUP_1 = [&R] (((1:0.030602,2:0.033203):0.167124,3:0.203691):0.343195,4:0); End;