dN/dS -1, in attempt to test purifying selection, CODEML PAML

Question

[scheng25]

I have a codon sequence and a tree topology. My goal is to calculate dN/dS for each branch, however, when I calculate the dN/dS using the code shown below, I run into the dS values as -1, however, this seems to be a mistake because if I shift the taxa that is at the top of the alignment, there are different dS values for the other taxa. I am not sure if this is the correct way to calculate the dN/dS for each branch? Additionally, is there a way to pull out dS values for each amino acid on a given branch?

Attached code here.

seqfile = PAMLTEST.phy * sequence data file name
treefile = Test.txt * tree structure file name
outfile = mannanasefinaloutput_2.mlc * main result file name
noisy = 9 * 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; -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, unrooted tree, 1: clock, rooted tree
aaDist = 0 * 0:equal, +:geometric; -:linear, {1-5:G1974,Miyata,c,p,v}
model = 1
NSsites = 0
* 0:one w; 1:NearlyNeutral; 2:PositiveSelection; 3:discrete;
* 4:freqs; 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ10:3normal
icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
Mgene = 0 * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all
fix_kappa = 1 * 1: kappa fixed, 0: kappa to be estimated
kappa = 1 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = 0 * initial or fixed omega, for codons or codon-based AAs
ncatG = 10 * # 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 = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
fix_blength = 1 * 0: ignore, -1: random, 1: initial, 2: fixed

[lieven.sterck]

hi scheng25,

Small educational note: I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[scheng25]

Thank you for that note! This is my first time posting!

[lieven.sterck]

no worries

better start sooner then later ;-)