#NEXUS
Begin trees; [Treefile saved Thu Oct 21 11:41:52 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At4g12230.1.cds.nex
>Branch-and-bound search settings:
> Optimality criterion = likelihood
> Likelihood settings:
> Transition/transversion ratio = 1.254 (kappa = 2.5346523)
> Assumed nucleotide frequencies (set by user):
> A=0.22450 C=0.21130 G=0.21900 T=0.34520
> Among-site rate variation:
> Assumed proportion of invariable sites = none
> Distribution of rates at variable sites = equal
> These settings correspond to the HKY85 model
> Number of distinct data patterns under this model = 28
> 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) = 749.68234
> 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 = 782.26970
> Number of trees retained = 1
> Time used = <1 sec (CPU time = 0.00 sec)
]
Translate
1 lgn_153067,
2 stgn_180947,
3 cangn_204269,
4 At4g12230.1
;
tree PAUP_1 = [&R] (((1:0.003049,2:0.006141):0.020046,3:0.023745):0.249795,4:0);
End;