#NEXUS 

begin trees;  [Treefile saved Fri Jan 01 13:02:54 1999]
[!
>Data file = C:\paup95NT\Trilliaceae\Combo.nex
>Heuristic search settings:
>   Optimality criterion = maximum likelihood
>      MLE settings:
>        Assumed nucleotide frequencies (empirical frequencies):
>          A = 0.28171
>          C = 0.19548
>          G = 0.20327
>          T = 0.31954
>        Number of substitution types = 2
>        All sites assumed to evolve at same rate
>        These settings correspond to the Felsenstein (1984) model (F84) or to the Hasegawa-Kishino-
>          Yano (1985) model (HKY) -- HKY model has been requested
>        Transition/transversion ratio = 2 (kappa = 4.17240)
>        Starting branch lengths obtained using Rogers-Swofford approximation method
>        Number of distinct data patterns under this model = 269
>        Molecular clock not enforced
>        Trees with approximate likelihoods 5% or further from the target score are rejected without
>          additional iteration
>        -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities
>      42 characters are eliminated (zapped)
>      102 characters are excluded
>   Starting tree(s) obtained via stepwise addition
>   Addition sequence: as-is
>   Number of trees held at each step during stepwise addition = 1
>   Branch-swapping algorithm: Tree-bisection-reconnection (TBR)
>   Steepest descent option not in effect
>   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
>
>Heuristic search completed
>   Total number of rearrangements tried = 5772
>   Score of best tree(s) found = 6013.46004
>   Number of trees retained = 1
>   Time used = 00:19:37.3
]
	translate
		1 T.rivale,
		2 D.fargesii,
		3 D.polyphylla,
		4 D.thibetica,
		5 D.violacea,
		6 K.japonica,
		7 P.incompleta,
		8 P.tetraphylla,
		9 P.verticillata,
		10 T.chloropetalum,
		11 T.decipiens,
		12 T.discolor,
		13 T.lancifolium,
		14 T.maculatum,
		15 T.petiolatum,
		16 T.recurvatum,
		17 T.reliquum,
		18 T.sessile,
		19 T.camschatcense,
		20 T.erectum,
		21 T.govanianum,
		22 T.grandiflorum,
		23 T.ovatum,
		24 T.pusillum,
		25 T.rugelii,
		26 T.undulatum
		;
tree PAUP_1 = [&U] (1:0.000000,(((((2:0.007339,(3:0.004990,5:0.007169):0.002787):0.002909,4:0.006957):0.011046,6:0.017621):0.003949,((7:0.007539,8:0.007133):0.004886,9:0.002950):0.005292):0.002618,((((((10:1.000e-08,(13:1.000e-08,16:1.000e-08):0.000461,14:0.000461,18:0.000922):0.000922,15:0.000462):0.000461,((11:0.001380,17:0.000460):0.000921,12:0.002312):0.002774):0.003404,((22:0.010148,23:0.008091):0.001958,24:0.011391):0.000527):0.002678,(19:0.005370,(20:0.000459,25:0.000458):0.004513):0.005600):0.003421,(21:0.006044,26:0.005558):0.001896):0.001849):0.028676);
end;