Tree File For Codeml Program Of Paml

Question

[Kushal Shah]

While running the codeml program of PAML, I gave a blank file as my tree input, and then a proper phylogenetic tree generated using PhyML. For both these files (one blank, and one proper tree), I am getting the same values of pairwise dN and dS (in the output files, 2NG.dN and 2NG.dS). This seems to imply that the codeml program is not using the tree file at all for its calculations.

I would be glad if somebody can help me in identifying the problem.

Thanks in advance, Kushal.

[Botond Sipos]

Which is the runmode you specified in the control file?

[Kushal Shah]

I use the runmode=0.

[Hranjeev]

why would you do a pairwise alignment with a blank tree?

[GR]

Just few quick questions about Codeml.

Can we study lineage-specific selection only on sequences that are single copy orthologs (or in simple words just have 1-1 relations). What should I do in case of multigene families? Does codeml works well in case of multi gene families? Do I have to extract 1-1 relations from these families and then input to codeml or the whole family can go as input?

Answer 1

[Suren]

2NG.dN and 2NG.dS (distance matrices files) are dS and dN estimates (synonymous and non-synonymous) calculated automatically while using codeml.

I think, such calculation do not need tree-file instead choose icode parameter for using correct codon-table for your sequences.

Note: codeml and Yn00 both produces output file for such calculation. yn00 uses Yang and Nielsen (2000) method for such calculation while codeml uses Nei & Gojobori 1986.

[Kushal Shah]

Thanks a lot, SK!