#NEXUS
Begin trees; [Treefile saved Wed Oct 20 16:31:11 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At1g23740.1.cds.nex
>Branch-and-bound search settings:
> Optimality criterion = likelihood
> Likelihood settings:
> Transition/transversion ratio = 0.9705 (kappa = 1.9798062)
> Assumed nucleotide frequencies (set by user):
> A=0.26470 C=0.15110 G=0.28920 T=0.29500
> 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 = 49
> 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 = 622.10079
> Number of trees retained = 1
> Time used = <1 sec (CPU time = 0.01 sec)
]
Translate
1 lgn_145147,
2 stgn_176591,
3 cangn_204056,
4 cgn_121897,
5 At1g23740.1
;
tree PAUP_1 = [&R] ((((1:0.010625,3:0.032355):0.005127,2:0.005320):0.117323,4:0.171030):0.220851,5:0);
End;