#NEXUS 

Begin trees;  [Treefile saved Tue Jan  8 00:05:13 2002]
[!
>Data file = /home/bjorn/bartonella/Glycolysis/Analysis15/Tpis/rednt.nex
>Bootstrap method with heuristic search:
>  Number of bootstrap replicates = 500
>  Starting seed = 75856721
>  Optimality criterion = distance (minimum evolution)
>    Negative branch lengths allowed, but set to zero for tree-score calculation
>    Distance measure = HKY85
>    Proportion of sites assumed to be invariable = 0.2438; identical sites removed proportionally to
>      base frequencies estimated from all sites (distances represent mean number of substitutions
>      over all sites)
>    Rates (for variable sites) assumed to follow gamma distribution with shape parameter = 1.8086
>    120 characters are excluded
>  Starting tree(s) obtained via stepwise addition
>  Addition sequence: random
>    Number of replicates = 10
>    Starting seed = 338309985
>  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
>  Zero-length branches not collapsed
>  'MulTrees' option in effect
>  Topological constraints not enforced
>  Trees are unrooted
>
>   500 bootstrap replicates completed
>   Time used = 01:03:08 (CPU time = 01:03:07.3)
]
	Translate
		1 Homo_sapiens,
		2 Rattus_norvegic,
		3 Culex_tarsalis,
		4 Schistosoma_man,
		5 Caenorhabditis,
		6 cy_Oryza_sativa,
		7 cy_Secale_cerea,
		8 cy_Coptis_japon,
		9 cp_Spinacia_ole,
		10 cp_Fragaria_ana,
		11 cp_Secale_cerea,
		12 Emericella_nidu,
		13 Saccharomyces_c,
		14 Odontella_sinen,
		15 Achlya_bisexual,
		16 Trypanosoma_bru,
		17 Giardia_lamblia,
		18 Plasmodium_falc,
		19 Entamoeba_histo,
		20 Neisseria_menin,
		21 Rhizobium_etli,
		22 Bartonella_hens,
		23 Mesorhizobium_l,
		24 Xanthobacter_fl,
		25 Caulobacter_cre,
		26 Agrobacterium_r,
		27 Mycobacterium_l,
		28 Buchnera_aphidi,
		29 Escherichia_col,
		30 Pseudomonas_syr,
		31 Chlamydia_pneum,
		32 Chlamydia_trach,
		33 Aquifex_aeolicu,
		34 Synechocystis_s,
		35 Bacillus_stearo,
		36 Borrelia_burgdo,
		37 Mycoplasma_floc,
		38 Mycoplasma_geni
		;
tree PAUP_1 = [&U] (1,2,((3,5,((6,7)78,8)97,((9,10)70,11)94,12,13,(14,15)60,16,17,18,19,20,21,(22,23)54,24,25,26,27,28,29,30,(31,32)91,33,(34,35)57,36,37,38)73,4)98)0;
End;