#NEXUS 

begin trees;  [Treefile saved Tue Dec 07 13:56:04 1999]
[!
>Data file = C:\WINNT\Profiles\jimmylin\Desktop\all_genomes\from-hegyi-991117-all\all_genomes_folds_paup3.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 = 2833
>   Score of best tree(s) found = 1.88384
>   Number of trees retained = 1
>   Time used = 0.28 sec
]
	translate
		1 Ctra,
		2 Cpne,
		3 Syne,
		4 Tpal,
		5 Bbur,
		6 Hinf,
		7 Ecol,
		8 Rpro,
		9 Hpyl,
		10 Mgen,
		11 Mpne,
		12 Bsub,
		13 Mtub,
		14 Aaeo,
		15 Aful,
		16 Mthe,
		17 Phor,
		18 Mjan,
		19 Scer,
		20 Cele
		;
tree PAUP_1 = [&U] (1:0.028431,2:0.027451,(((((((3:0.076990,(12:0.060131,13:0.054575):0.014187):0.014062,(6:0.070752,7:0.123366):0.029248):0.005352,(19:0.073856,20:0.164379):0.128733):0.029191,14:0.072199):0.011134,((15:0.073789,(17:0.073366,18:0.058987):0.011505):0.005785,16:0.059988):0.075950):0.016258,(8:0.084641,9:0.068301):0.004943):0.042764,((4:0.051144,5:0.063562):0.017188,(10:0.022222,11:0.016013):0.093107):0.015704):0.044590);
end;