#NEXUS 

Begin trees;  [Treefile saved Wed Oct 20 16:50:28 2004]
[!
>Data file = /home/fw38/blast/result/SGN_COSII/phylogeny-r2.0/At1g52980.1.cds.nex
>Branch-and-bound search settings:
>  Optimality criterion = likelihood
>    Likelihood settings:
>      User-specified substitution rate matrix =
>                  -   1.000000   3.033300   1.000000
>           1.000000          -   1.000000   6.324200
>           3.033300   1.000000          -   1.000000
>           1.000000   6.324200   1.000000          -
>      Assumed nucleotide frequencies (set by user):
>        A=0.29930  C=0.17680  G=0.23270  T=0.29120
>      Among-site rate variation:
>        Assumed proportion of invariable sites  = none
>        Distribution of rates at variable sites = gamma (discrete approximation)
>          Shape parameter (alpha)   = 0.8189
>          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 = 73
>      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 = 1680.50711
>   Number of trees retained = 1
>   Time used = <1 sec (CPU time = 0.11 sec)
]
	Translate
		1 lgn_145427,
		2 stgn_173763,
		3 cangn_197965,
		4 cgn_121609,
		5 At1g52980.1
		;
tree PAUP_1 = [&R] ((((1:0.011546,2:0.007415):0.028006,3:0.018547):0.109377,4:0.081314):0.169159,5:0);
End;