1 seqfile = lysozymeSmall.txt
\r
2 treefile = lysozymeSmall.trees
\r
5 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
\r
6 verbose = 1 * 1: detailed output, 0: concise output
\r
7 runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
\r
8 * 3: StepwiseAddition; (4,5):PerturbationNNI
\r
10 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
\r
11 CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
\r
12 clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree
\r
14 * models for codons:
\r
15 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
\r
17 NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive
\r
18 icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
\r
20 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
\r
21 kappa = 2 * initial or fixed kappa
\r
22 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
\r
23 omega = 2 * initial or fixed omega, for codons or codon-transltd AAs
\r
25 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
\r
26 alpha = .0 * initial or fixed alpha, 0:infinity (constant rate)
\r
27 Malpha = 0 * different alphas for genes
\r
28 ncatG = 4 * # of categories in the dG or AdG models of rates
\r
30 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
\r
31 RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0)
\r
32 method = 0 * 0: simultaneous; 1: one branch at a time
\r
35 * Specifications for duplicating results for the small data set in table 1
\r
36 * of Yang (1998 MBE 15:568-573).
\r
37 * see the tree file lysozyme.trees for specification of node (branch) labels
\r