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