#NEXUS 

begin trees;  [Treefile saved Sun Dec 20 13:15:22 1998]
[!
>Data file = C:\paup95NT\Trilliaceae\ITS.nex
>Heuristic search settings:
>   Optimality criterion = maximum likelihood
>      MLE settings:
>        Assumed nucleotide frequencies (empirical frequencies):
>          A = 0.21067
>          C = 0.24399
>          G = 0.32677
>          T = 0.21856
>        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 = 4.06973)
>        Starting branch lengths obtained using Rogers-Swofford approximation method
>        Number of distinct data patterns under this model = 194
>        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
>      27 characters are eliminated (zapped)
>   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 = 200
>   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 = 5603
>   Score of best tree(s) found = 2755.66433
>   Number of trees retained = 1
>   Time used = 00:11:09.8
]
	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,(((((2,4),(3,5)),6),((7,8),9)),(((((10,13,14,15,16,18),((11,17),12)),((22,24),23)),(19,(20,25))),(21,26))));
end;