Entering edit mode
6.4 years ago
Mehmet
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820
Dear All,
I have done several analysis to find dN/dS ratio in six species.
I found one-to-one orthologs (by orthofinder)
I did codon-based alignments of the orthologs that produced .paml format alignments.
I did protein alignment of the orthologs.
Now I would like to have your advice on:
How to concanate all paml files that are used in codeml.?
To be used in codeml (as tree file) do I need to perform phylogenetic of those .paml files? or it is fine to use all.paml files only in codeml?
Hi Mehmet,
I think calculating dn/ds per alignment is good. You can create quick trees for the alignment as input of codeml, otherwise you could let the programme do it.
I performed dN/dS analysis using alignments of all orthologs (~5000) together.
Maybe by setting mgene = in the control file?
Please how can I get the alignment for all orthologs.? What steps do I have to follow?
PS: I have already run orthofinder and a lot of files were generated. Please advice.
Thanks
Steps that you need to follow are:
I have performed steps 1 and 2. I also see that the alignment of protein sequences is in the MultipleSequenceAlignments folder.
But I am a bit confused about step 3. If you say I should get alignment of CDS, do you mean the alignment of CDS that were identified as orthologs ? I would be grateful if you can give a bit of details. Thanks
But I am a bit confused about step 3. If you say I should get alignment of CDS, do you mean the alignment of CDS that were identified as orthologs ? I would be grateful if you can give a bit of details.
Yes, you should use the same ortholog (single copy ones) CDS sequences. Please let me know if you need more help.
Hi Sishuo,
I would like to have your suggestion:
I have run codeml with the control file below;
What I need is how I can get dN/dS ratio
When I typed
grep omega mlc > omega.txt
omega.txt
file has nothing.Hi Mehmet,
Sorry, not sure.
Have you got anything in the mlc file? Or was the analysis disrupted?
By the way, there was a typo in "eqfile = all.paml".
the analysis did not disrupt. Yes, I have star tree and best tree values for each gene. But I did not get omega values. Is it fine to use a best tree that has highest likelihood value as a tree file in next codeml run?
I think that should work.