dN/dS -1, in attempt to test purifying selection, CODEML PAML
0
0
Entering edit mode
22 months ago
scheng25 ▴ 10

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
codeml paml • 735 views
ADD COMMENT
1
Entering edit mode

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:

101010 Button

ADD REPLY
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode

no worries

better start sooner then later ;-)

ADD REPLY

Login before adding your answer.

Traffic: 2343 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6