#NEXUS 

Begin trees;  [Treefile saved Fri Feb 11 11:04:20 2005]
[!
>Data file = C:\FimH\fimh-asm-unique.nxs
>Heuristic search settings:
>  Optimality criterion = likelihood
>    Likelihood settings:
>      User-specified substitution rate matrix =
>                  -   1.655466   4.388160   1.219681
>           1.655466          -   0.862399   4.759818
>           4.388160   0.862399          -   1.000000
>           1.219681   4.759818   1.000000          -
>      Assumed nucleotide frequencies (set by user):
>        A=0.23674  C=0.22071  G=0.25980  T=0.28275
>      Among-site rate variation:
>        Site-specific rates assigned based on values previously estimated
>        using character-partition "by codon"
>      These settings correspond to the GTR+SS model
>      Number of distinct data patterns under this model = 93
>      Molecular clock not enforced
>      Starting branch lengths obtained using Rogers-Swofford approximation
>        method
>      Trees with approximate likelihoods 5% or further from the target score
>        are rejected without additional iteration
>      Branch-length optimization = one-dimensional Newton-Raphson with pass
>                                   limit=20, delta=1e-006
>      -ln L (unconstrained) = 1757.93210
>  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
>  Initial swapping on tree 1 already in memory
>  Steepest descent option not in effect
>  Initial 'MaxTrees' setting = 1200 (will be auto-increased by 100)
>  Branches collapsed (creating polytomies) if branch length is less than or
>     equal to 1e-008
>  'MulTrees' option in effect
>  Topological constraints not enforced
>  Trees are unrooted
>
>Heuristic search completed
>   Total number of rearrangements tried = 21139
>   Score of best tree(s) found = 2291.77631
>   Number of trees retained = 1
>   Time used = 00:01:59.1
]
	Translate
		1 JJf10n2,
		2 JJF16,
		3 JJV2,
		4 JJP114,
		5 JJF25,
		6 jjc53n6,
		7 JJF18,
		8 JJB12,
		9 bpnPAP1071,
		10 JJB6,
		11 JJV18,
		12 bpnpap1094n2,
		13 JJP172,
		14 JJF2,
		15 jjp103,
		16 JJV16,
		17 bpn1224n2,
		18 JJF28,
		19 JJF1n2,
		20 JJP55n2,
		21 JJC220,
		22 JJF9n4,
		23 ECOR2,
		24 JJP90,
		25 JJP199,
		26 JJB28,
		27 JJC102,
		28 JJF30,
		29 JJF21,
		30 JJF15,
		31 JJB2n6,
		32 JJC179,
		33 JJF8n5,
		34 JJV20,
		35 JJB18,
		36 JJF13,
		37 jjf23,
		38 JJV12,
		39 jjb24n6,
		40 JJB20,
		41 JJC163,
		42 JJP44n6,
		43 JJC267
		;
tree PAUP_1 = [&U] (1,(2,3,4,(5,((6,7,8,9),((((10,11),12,13),14,15),16)),((17,18,((19,20),21)),(((((22,24),23),(25,26),(27,28)),((29,30),(((31,32),((33,42),34)),((35,36),(37,38,39)),(40,41)))),43)))));
End;