#NEXUS
Begin trees; [Treefile saved Wed Oct 20 14:41:44 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r3.0/At4g17040.1.cds.nex
>Branch-and-bound search settings:
> Optimality criterion = likelihood
> Likelihood settings:
> User-specified substitution rate matrix =
> - 1.000000 2.454600 2.032000
> 1.000000 - 2.032000 2.454600
> 2.454600 2.032000 - 1.000000
> 2.032000 2.454600 1.000000 -
> Assumed nucleotide frequencies (set by user):
> A=0.24300 C=0.24320 G=0.20700 T=0.30680
> Among-site rate variation:
> Assumed proportion of invariable sites = none
> Distribution of rates at variable sites = gamma (discrete approximation)
> Shape parameter (alpha) = 0.6341
> Number of rate categories = 4
> Representation of average rate for each category = mean
> These settings correspond to the GTR+G model
> Number of distinct data patterns under this model = 70
> 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) = 1768.21324
> 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 = 1836.31193
> Number of trees retained = 1
> Time used = <1 sec (CPU time = 0.10 sec)
]
Translate
1 lgn_214346,
2 stgn_175364,
3 cangn_197513,
4 cgn_129203,
5 At4g17040.1
;
tree PAUP_1 = [&R] ((((1:0,4:0):0.024012,2:0.008150):0.079376,3:0.057737):0.541795,5:0);
End;