1
seqfile = stewart.aa * sequence data filename
2
treefile = stewart.trees * tree structure file name
4
outfile = mlc * main result file name
5
noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
6
verbose = 0 * 0: concise; 1: detailed, 2: too much
7
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
8
* 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
10
seqtype = 2 * 1:codons; 2:AAs; 3:codons-->AAs
11
aaRatefile = dat/wag.dat * only used for aa seqs with model=empirical(_F)
12
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
14
model = 3 * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
15
* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
16
Mgene = 0 * aaml: 0:rates, 1:separate;
18
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
19
alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
20
Malpha = 0 * different alphas for genes
21
ncatG = 2 * # of categories in dG of NSsites models
23
clock = 0 * 0:no clock, 1:global clock; 2:local clock; 3:TipDate
24
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
25
RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
27
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
28
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
29
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
31
* These codes correspond to transl_table 1 to 11 of GENEBANK.
34
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
36
method = 0 * 0: simultaneous; 1: one branch at a time
added
removed
aaml.ctl
