1 seqfile = MouseLemurs.nuc
\r
2 treefile = MouseLemurs.trees
\r
4 outfile = mlc * main result file name
\r
5 noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
\r
6 verbose = 1 * 0: concise; 1: detailed, 2: too much
\r
9 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
\r
15 clock = 6 * 0:no clock, 1:global clock; 2:local clock
\r
16 icode = 1 * 0:universal code; 1:mammalian mt; 2-10:see below
\r
23 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
\r
24 alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
\r
25 ncatG = 3 * # of categories in dG of NSsites models
\r
27 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
\r
28 RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
\r
31 * cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
\r
32 method = 1 * 0: simultaneous; 1: one branch at a time
\r
33 fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
\r