Question: Problem with CODEML parameters
gravatar for aeonswhisper
3 months ago by
aeonswhisper0 wrote:

I am undergrad student, and I am studying the evolution of one gene in a subgroup of Drosophila species. For that, I am comparing the sequence of this gene of 12 Drosophila species, and I am looking for signs of selection. I have populational data from D. melanogaster and D. simulans to run HKA test, and I am also running Tajima relative rate tests in some points of the phylogeny.

I expect that this gene is under purifying selection (I'll compare the dn/ds with the average dn/ds of the whole genome)

What I did before was run dn/ds calculations on SNAP, and I got the dn/ds between Dmel and each of the other 11 species, but that didn't make sense because it didn't take phylogeny in consideration.

So what I need to do now is to find the dn/ds for this gene, and for that I am using CODEML, but I am confused about the model I should run. I have read the PAML manual, but I am still uncertain about what parameters I should use.

Should I run different models and then compare them?


ADD COMMENTlink written 3 months ago by aeonswhisper0

Look through the whole biostars site – you are not alone, there are some similar posts on this problem.

To find other posts. go to the upper left hand corner, press 'LATEST'

and type your question to the line in the middle of the page.

As to your question - try at least one model. Get some output,

analyze it, and if you are not satisfied, try another model. Below

there are posts on your question.

Codeml- Dn/Ds High Due To The Low Ds

Calculate Average Dn And Ds For Gene Families

[solved] BioPython: CodeML FileNotFoundError: [WinError 2]

CodeML Troubleshooting Help

Error running certain PAML - CodeML sequences

Read PAML-manual again - the ref is in the post below

dN/dS ratio (omega)

Very anomalous dN/dS output trouble in PAML

dN/dS output trouble in PAML

Need Help With Understanding Codeml Output

Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data

And always look at the right panel for other close posts.

ADD REPLYlink modified 3 months ago • written 3 months ago by natasha.sernova3.4k

Thank you. I am not totally lost with this any more.

ADD REPLYlink written 3 months ago by aeonswhisper0
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