#NEXUS 

Begin trees;  [Treefile saved Wednesday, July 18, 2012  4:55 PM]
[!
>Data file = 2Bromus tef tub ordermodeltest.
>Heuristic search settings:
>  Optimality criterion = likelihood
>    Likelihood settings:
>      User-specified substitution rate matrix =
>                  -   0.864204   2.814229   1.167399
>           0.864204          -   0.867062   3.866232
>           2.814229   0.867062          -   1.000000
>           1.167399   3.866232   1.000000          -
>      Assumed nucleotide frequencies (set by user):
>        A=0.24967  C=0.26658  G=0.23635  T=0.24740
>      Among-site rate variation:
>        Assumed proportion of invariable sites  = 0.130511
>        Distribution of rates at variable sites = gamma (discrete approximation)
>          Shape parameter (alpha)   = 0.871432
>          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 = 401
>      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-06
>      -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities
>  Starting tree(s) obtained via stepwise addition
>  Addition sequence: random
>    Number of replicates = 1
>    Starting seed = 620577127
>  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 = 100 (will be auto-increased by 100)
>  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 = 122969
>   Score of best tree(s) found = 4588.34917
>   Number of trees retained = 1
>   Time used = 22:20:29.8
]
	Translate
		1 P2C2_typhina,
		2 P3C1_typhina,
		3 P4C2_typhina,
		4 P6_typhina,
		5 P7_typhina,
		6 P10C2_typhina,
		7 P15C2_typhina,
		8 P2C1_elymi,
		9 P3C2_amarillans,
		10 P4C1_amarillans,
		11 P5C1_amarillans,
		12 P9C2_amarillans,
		13 P10C1_elymi,
		14 P12C1_amarillans,
		15 P15C1_elymi,
		16 AF231231_Epichloe_typhina__Pp,
		17 AF231222_Epichloe_typhina__Ao,
		18 AF231227_Epichloe_typhina__Php,
		19 AF231226_Epichloe_typhina__Php,
		20 AF231221_Epichloe_typhina__Lp,
		21 AF231223_Epichloe_typhina__Bp,
		22 AF231230_Epichloe_typhina__Pn,
		23 AF231228_Epichloe_typhina__Ps,
		24 HM138506_Neotyphodium_schardlii__Ca,
		25 HM138507_Neotyphodium_schardlii__Ca,
		26 AF231207_Epichloe_clarkii__Hl,
		27 AF231218_Epichloe_sylvatica__Bs,
		28 AF231201_Epichloe_brachyelytri__Bee,
		29 AF231200_Epichloe_brachyelytri__Bee,
		30 AF231195_Epichloe_baconii__At,
		31 AF231193_Epichloe_baconii__As,
		32 AF231196_Epichloe_baconii__Cv,
		33 AF457504_Epichloe_amarillans__So,
		34 AF457505_Epichloe_amarillans__Ah,
		35 AF457506_Epichloe_amarillans__Ap,
		36 AF231213_Epichloe_festucae__Fl,
		37 AF231210¬_Epichloe_festucae__Frr,
		38 AF457498_E._elymi__Ev,
		39 AF231202_Epichloe_bromicola__Be,
		40 AF231217_Epichloe_glyceriae__Gs,
		41 AF231216_Epichloe_glyceriae__Gs,
		42 DQ134034_Epichloe_yangzii__Rk,
		43 DQ134030_Epichloe_yangzii__Rk,
		44 JQ756452_Epichloe_poae__Psj,
		45 AF457509_N_chisosum__Se,
		46 AF457508_N_chisosum__Se,
		47 AF457510_N_chisosum__Se,
		48 AF457541_N_occultans__Lrr,
		49 AF457542_N_occultans__Lrr,
		50 AY707673_N_tembladerae__Ph,
		51 AY707691_N_tembladerae__Ph,
		52 AY707677_N_tembladerae__Bs,
		53 AY707658_N_tembladerae__Bs,
		54 FJ190584_N_tembladerae__Ba,
		55 FJ190576_N_tembladerae__Ba,
		56 AY707675_N_tembladerae__Fh,
		57 AY707661_N_tembladerae__Fh,
		58 AF457518_Neotyphodium__Evi,
		59 AF457517_Neotyphodium__Bp,
		60 FJ190572_N_pampeanum__Ba,
		61 FJ190580_N_pampeanum__Ba,
		62 FJ190570_N_pampeanum__Ba,
		63 FJ190578_N_pampeanum__Ba,
		64 AF457513_Neotyphodium_Pau,
		65 AF457514_Neotyphodium_Pau,
		66 AF457515_Neotyphodium__Fpa,
		67 AF457516_Neotyphodium__Fpa,
		68 AF532924_Neotyphodiun__Hbo,
		69 AF532923_Neotyphodium__Hbo,
		70 AY163833_Neotyphodium__Hbo,
		71 AF457524_Neotyphodium__Hbo,
		72 AF457534_Neotyphodium__Sro,
		73 AF457533_Neotyphodium__Sro,
		74 AY707683_Neotyphodium__Phc,
		75 AY707672_Neotyphodium__Phc,
		76 JX028260_N_coenophialum__La,
		77 JX028261_N_coenophialum__La,
		78 JX028262_N_coenophialum__La,
		79 JX028266_Neotyphodium__Fa2,
		80 JX028267_Neotyphodium__Fa2,
		81 AF457529_Neotyphodium_Fa3,
		82 AF457530_Neotyphodium_Fa3,
		83 AF457532_Neotyphodium_Fa2,
		84 AF457531_Neotyphodium_Fa2
		;
tree PAUP_1 = [&U] (1,((((2,3,25,74),22,65),4,5,7,((((((((((8,13,15),((38,69),64),59,72),(((39,(42,43)),49),(45,71))),(40,41)),(28,29)),(((((9,10,11,12,14),75),((((33,34),((35,58),68)),46),67)),32),((30,31),(48,78,(80,82,84))),(36,37,51,53,55,57,(60,62),73,77,79,83))),((((17,70),18),((19,23),((20,26),81))),(21,27))),(16,24,47)),(61,63),76),44),(50,52,54,56),66),6));
End;