I finally, and somewhat accidentally, managed to solve the problem. I'm not sure exactly what solved the problem, so here is a summary of my input:
Tree file:
(Human, (Green_ano #1, Chicken #2))
Control file (I have a script that adds the file names):
seqfile = * sequence data filename
treefile = * tree structure file name
outfile = * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
verbose = 0 * 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 = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 0 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
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 = dat/jones.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 1
* models for codons:
* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
* 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
* 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
* 13:3normal>0
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 3 * 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-based 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 = 8 * # of categories in dG of NSsites models
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
method = 1 * Optimization method 0: simultaneous; 1: one branch a time
My input files are in sequential phylip format.
Hello smrupp16!
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Don't close this post yourself. Instead accept the answer you posted below (use tick mark, and any other answers, if applicable). That would be the best way to indicate that the problem has found an answer.
I re-opened the post. It was probably closed because OP thought that was how to mark something solved, though the "close post" option is for something entirely different (mainly off-topic posts).