#NEXUS 

begin trees;  [Treefile saved Mon Dec 20 14:54:06 1999]
[!
>Data file = F:\Jimmy\20 genomes\sfam_tree\all_genomes_sfams_paup.nex
>Heuristic search settings:
>   Optimality criterion = distance (minimum evolution)
>      Negative branch lengths allowed, but set to zero for tree-score
>         calculation
>      Distance measure = mean character difference
>   Starting tree(s) obtained via neighbor-joining
>   Branch-swapping algorithm: tree-bisection-reconnection (TBR)
>   Steepest descent option not in effect
>   Initial 'MaxTrees' setting = 100
>   Zero-length branches not collapsed
>   'MulTrees' option in effect
>   Topological constraints not enforced
>   Trees are unrooted
>
>NOTE: Random-addition-sequence option is ignored when starting trees are
>      obtained using neighbor-joining.
>
>Heuristic search completed
>   Total number of rearrangements tried = 2616
>   Score of best tree(s) found = 1.96489
>   Number of trees retained = 1
>   Time used = 0.27 sec
]
	translate
		1 Aful,
		2 Mjan,
		3 Mthe,
		4 Phor,
		5 Scer,
		6 Cele,
		7 Aaeo,
		8 Syne,
		9 Ecol,
		10 Bsub,
		11 Mtub,
		12 Hinf,
		13 Hpyl,
		14 Mgen,
		15 Mpne,
		16 Bbur,
		17 Tpal,
		18 Ctra,
		19 Cpne,
		20 Rpro
		;
tree PAUP_1 = [&U] (1:0.071474,(2:0.069056,4:0.081481):0.003795,(3:0.064203,((5:0.073118,6:0.156989):0.129916,(((7:0.062366,8:0.098925):0.006336,((9:0.138112,12:0.070490):0.020497,(10:0.083274,11:0.073716):0.019288):0.025922):0.018181,(13:0.067588,((((14:0.024253,15:0.014456):0.089113,(16:0.072999,17:0.056033):0.008737):0.024808,(18:0.024970,19:0.024492):0.044547):0.020501,20:0.090405):0.026173):0.017776):0.019948):0.061863):0.009084);
end;