control_file.ctl

seqfile = TargetSequences.out.phy    * sequence data filename
treefile = TargetSequences.out.tree   * tree structure file name
outfile = TargetSequences.out.mlc    * main result file name

noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
verbose = 2  * 0: concise; 1: detailed, 2: too much
runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

seqtype = 2  * 1:codons; 2:AAs; 3:codons-->AAs

clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
aaRatefile = ./jones.dat  	* only used for aa seqs with model=empirical(_F)
				* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

model = 2
	* models for codons:
	* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
	* models for AAs or codon-translated AAs:
	* 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
	* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
Mgene = 0  * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff             
           * AA: 0:rates, 1:separate

fix_alpha = 0   * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0.5 	* initial or fixed alpha, 0:infinity (constant rate)
Malpha = 1   	* different alphas for genes
ncatG = 4   	* # of categories in dG of NSsites models

getSE = 0  	* 0: don't want them, 1: want S.E.s of estimates

RateAncestor = 1  	* (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

Small_Diff = .5e-6
cleandata = 0  	* remove sites with ambiguity data (1:yes, 0:no)?
method = 1  	* Optimization method 0: simultaneous; 1: one branch a time


* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.