#NEXUS 

Begin trees;  [Treefile saved Sat Oct 27 16:34:37 2012]
[!
>Data file = C:\Users\Jadson\Desktop\TreeBase\Favolaschia_alinhamento.nexus
>Heuristic search settings:
>  Optimality criterion = likelihood
>    Likelihood settings:
>      User-specified substitution rate matrix =
>                  -   1.654600   3.680900   2.005500
>           1.654600          -   1.079800   6.806200
>           3.680900   1.079800          -   1.000000
>           2.005500   6.806200   1.000000          -
>      Assumed nucleotide frequencies (set by user):
>        A=0.22160  C=0.20140  G=0.22630  T=0.35070
>      Among-site rate variation:
>        Assumed proportion of invariable sites  = 0.2422
>        Distribution of rates at variable sites = gamma (discrete
>                                                  approximation)
>          Shape parameter (alpha)   = 0.7113
>          Number of rate categories = 4
>          Representation of average rate for each category = mean
>      These settings correspond to the GTR+G+I model
>      Number of distinct data patterns under this model = 341
>      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) = unavailable due to missing-data and/or
>                              ambiguities
>  Starting tree(s) obtained via neighbor-joining
>  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
>  Steepest descent option not in effect
>  Initial 'MaxTrees' setting = 100 (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
>
>NOTE: Random-addition-sequence option is ignored when starting trees are
>      obtained using neighbor-joining.
>
>Heuristic search completed
>   Total number of rearrangements tried = 10917
>   Score of best tree(s) found = 3297.25982
>   Number of trees retained = 1
>   Time used = 00:07:27.1
]
	Translate
		1 Favolaschia_cinnabarina_JX987669,
		2 Favolaschia_luteoaurantiaca_JX987667,
		3 Favolaschia_sp_JX987668,
		4 Favolaschia_sp_DUKE2708_DQ026234,
		5 Favolaschia_sp_DUKE2876_DQ026235,
		6 Favolaschia_sp_DUKE3195_DQ026236,
		7 Favolaschia_tonkinensis_DQ026247,
		8 Favolaschia_pustulosa_DQ026245,
		9 Favolaschia_pustulosa_DQ026254,
		10 Favolaschia_sprucei_DQ026246,
		11 Favolaschia_peziziformis_DQ026255,
		12 Favolaschia_austrocyatheae_DQ026257,
		13 Favolaschia_cyatheae_DQ026256,
		14 Favolaschia_calocera_DQ026238,
		15 Favolaschia_calocera_DQ026250,
		16 Favolaschia_calocera_DQ026239,
		17 Favolaschia_calocera_DQ026240,
		18 Favolaschia_calocera_DQ026252,
		19 Favolaschia_calocera_DQ026253,
		20 Favolaschia_calocera_DQ026251,
		21 Favolaschia_calocera_DQ026248,
		22 Favolaschia_calocera_DQ026249,
		23 Favolaschia_aurantiaca_JX987670,
		24 Favolaschia_calocera_DQ026237,
		25 Favolaschia_sp_TH1018_DQ026241,
		26 Favolaschia_varariotecta_DQ026243,
		27 Favolaschia_varariotecta_DQ026244,
		28 Favolaschia_cinnabarina_DQ026242,
		29 Panellus_minimus_DQ026258,
		30 Panellus_pusillus_AF289061,
		31 Panellus_stypticus_AF289069
		;
tree PAUP_1 = [&R] (((((1:0,28:0):0.018684,((2:0.007179,23:0.120721):0.011471,((((((14:0,20:0,21:0,22:0,24:0):0.001780,15:0):0.003587,(18:0.003725,19:0.003691):0.001761):0.001805,16:0.005161):0.003418,17:0.001990):0.013811,25:0.021243):0.004701):0.013481):0.009483,(3:0.009228,(26:0,27:0.001830):0.078968):0.002688):0.027219,(((((((4:0,5:0):0.001425,6:0):0.020622,9:0.007860):0.004291,(7:0.002857,8:0.004036):0.004115):0.030068,(11:0.032153,12:0.039024):0.015570):0.008466,13:0.044072):0.014406,10:0.039728):0.005809):0.142523,29:0.044683,(30:0.026748,31:0.049869):0.084107):0;
End;