#NEXUS
Begin trees; [Treefile saved Thu Oct 21 13:16:45 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At5g49060.1.cds.nex
>Branch-and-bound search settings:
> Optimality criterion = likelihood
> Likelihood settings:
> Transition/transversion ratio = 1.3917 (kappa = 2.7659522)
> Assumed nucleotide frequencies (set by user):
> A=0.28760 C=0.12820 G=0.29680 T=0.28740
> Among-site rate variation:
> Assumed proportion of invariable sites = none
> Distribution of rates at variable sites = gamma (discrete approximation)
> Shape parameter (alpha) = 0.4091
> 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 = 101
> 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 = 1315.41149
> Number of trees retained = 1
> Time used = 1 sec (CPU time = 0.06 sec)
]
Translate
1 lgn_152380,
2 cangn_204255,
3 cgn_132594,
4 At5g49060.1
;
tree PAUP_1 = [&R] ((1:1.716944,(2:0.169914,3:0.199534):0.336119):0.411519,4:0);
End;