#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;