#NEXUS 

begin trees;  [Treefile saved Mon Dec 28 13:17:20 1998]
[!
>Data file = C:\paup95NT\Trilliaceae\matK.nex
>Heuristic search settings:
>   Optimality criterion = maximum likelihood
>      MLE settings:
>        Assumed nucleotide frequencies (empirical frequencies):
>          A = 0.30998
>          C = 0.17616
>          G = 0.15410
>          T = 0.35976
>        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 = 4.47548)
>        Starting branch lengths obtained using Rogers-Swofford approximation method
>        Number of distinct data patterns under this model = 93
>        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
>      7 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 = 500
>   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 = 6624
>   Score of best tree(s) found = 2941.08701
>   Number of trees retained = 1
>   Time used = 00:05:04.5
]
	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,(((((2:0.000647,3:0.000647,5:0.000647):0.002917,4:0.001630):0.000642,6:0.002925):0.001609,((7:0.001289,8:1.000e-08):0.004408,9:0.002068):0.001910):0.001322,(((((((10:1.000e-08,(13:1.000e-08,16:1.000e-08):0.000645,14:0.000646,18:1.000e-08):0.001292,((11:1.000e-08,17:0.000645):0.000646,12:0.001292):0.001292,15:1.000e-08):0.001295,(22:0.001934,23:1.000e-08):0.002584):0.000641,24:0.002590):0.001290,(19:0.000804,(20:0.000640,25:0.000640):0.002413):0.001287):0.000648,21:0.007147):0.000644,26:0.004540):0.000647):0.010397);
end;