#NEXUS 

Begin trees;  [Treefile saved Wed Jul 11 17:38:14 2001]
[!
>Data file = /home/bjorn/bartonella/Glycolysis/Analysis14/E_edd/rednt.nex
>Bootstrap method with fast-heuristic search:
>  Number of bootstrap replicates = 100
>  Starting seed = 1070116741
>  Optimality criterion = maximum likelihood
>    523 characters are excluded
>    Likelihood settings:
>      User-specified substitution rate matrix =
>                  -          1      1.803          1
>                  1          -          1      1.471
>              1.803          1          -          1
>                  1      1.471          1          -
>      Assumed nucleotide frequencies (set by user):
>        A=0.27670  C=0.26200  G=0.27290  T=0.18840
>      Among-site rate variation:
>        Assumed proportion of invariable sites  = none
>        Distribution of rates at variable sites = gamma (discrete
>                                                  approximation)
>          Shape parameter (alpha)   = 0.4876
>          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 = 485
>      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
>  Starting tree(s) obtained via stepwise addition with random addition sequence
>  Branch-swapping algorithm: none
>  Branches collapsed (creating polytomies) if branch length is less than or
>     equal to 1e-08
>  Topological constraints not enforced
>  Trees are unrooted
>
>   100 bootstrap replicates completed
>   Time used = 01:09:16 (CPU time = 00:23:31.0)
]
	Translate
		1 Escherichia_col,
		2 Pseudomonas_aer,
		3 Zymomonas_mobil,
		4 Caulobacter_cre,
		5 Rhizobium_melil,
		6 Mesorhizobium_l,
		7 Bartonella_hens,
		8 Agrobacterium_r,
		9 1Helicobacter_p,
		10 2Helicobacter_p
		;
tree PAUP_1 = [&U] (7,(1,2,3,4,8,(9,10)100)66,(5,6)80)0;
End;