#NEXUS 

Begin trees;  [Treefile saved Tue Jan  8 02:26:52 2002]
[!
>Data file = /home/bjorn/bartonella/Glycolysis/Analysis15/Pyruvate/rednt.nex
>Heuristic search settings:
>  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 = 0.2244; 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 = 1.3741
>    196 characters are excluded
>  Starting tree(s) obtained via stepwise addition
>  Addition sequence: random
>    Number of replicates = 500
>    Starting seed = 410998892
>  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
>
>Heuristic search completed
>   Total number of rearrangements tried = 160925
>   Score of best tree(s) found = 4.10491
>   Number of trees retained = 1
>   Time used = 7 sec (CPU time = 7.21 sec)
]
	Translate
		1 cp_Porphyra_purpurea,
		2 Synechocystis_sp.,
		3 Thiobacillus_ferrooxidans,
		4 Rhizobium_meliloti,
		5 Mesorhizobium_loti,
		6 Bartonella_henselae,
		7 Azorhizobium_caulinodans,
		8 Caulobacter_crescentus,
		9 Zymomonas_mobilis,
		10 Rickettsia_prowazekii,
		11 Ascaris_suum,
		12 Caenorhabditis_elegans,
		13 Mus_musculus,
		14 Rattus_norvegicus,
		15 Homo_sapiens,
		16 Sus_scrofa,
		17 Trypanosoma_cruzi,
		18 Kluyveromyces_lactis,
		19 Saccharomyces_cerevisiae,
		20 Schizosaccharomyces_pombe,
		21 Arabidopsis_thaliana,
		22 Pisum_sativum,
		23 Solanum_tuberosum,
		24 mtZea_mays,
		25 Chlamydia_trachomatis,
		26 Chlamydophila_pneumoniae
		;
tree PAUP_1 = [&U] (1:0.072239,2:0.076555,((3:0.267600,(25:0.062608,26:0.084196):0.457639):0.048724,(((((((4:0.020824,7:0.127938):0.008299,5:0.034531):0.015565,6:0.030872):0.040881,8:0.067518):0.027057,9:0.128257):0.019552,(((((11:0.111320,12:0.036088):0.103681,((18:0.036607,19:0.016916):0.130561,20:0.154808):0.050875):0.033496,((21:0.023047,(22:0.050356,23:0.036850):0.025711):0.013052,24:0.058503):0.129651):0.013289,((13:-0.001047,(14:0.005666,16:0.010300):0.003669):0.003737,15:0.000322):0.182179):0.024713,17:0.299343):0.142010):0.040612,10:0.235357):0.237388):0.303949);
End;