#NEXUS 

Begin trees;  [Treefile saved Thu Oct 21 12:05:26 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At4g30930.1.cds.nex
>Branch-and-bound search settings:
>  Optimality criterion = likelihood
>    Likelihood settings:
>      Assumed nucleotide frequencies (set by user):
>        A=0.28930  C=0.16490  G=0.31190  T=0.23390
>      Among-site rate variation:
>        Assumed proportion of invariable sites  = none
>        Distribution of rates at variable sites = gamma (discrete approximation)
>          Shape parameter (alpha)   = 0.4498
>          Number of rate categories = 4
>          Representation of average rate for each category = mean
>      These settings correspond to the F81+G model
>      Number of distinct data patterns under this model = 63
>      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) = 668.22444
>  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 = 763.20312
>   Number of trees retained = 2
>   Time used = 1 sec (CPU time = 0.26 sec)
]
	Translate
		1 lgn_147886,
		2 stgn_175188,
		3 cangn_203042,
		4 cgn_129790,
		5 At4g30930.1
		;
tree PAUP_1 = [&R] (((1:0.019349,2:0.004949,3:0.099237):0.082146,4:0.543237):0.521374,5:0);
tree PAUP_2 = [&R] ((((1:0.019349,2:0.004949):1.664e-06,3:0.099236):0.082121,4:0.543264):0.521393,5:0);
End;