Available software for checking all species have a 4d site for a particular codon in alignment?

Question

[RoryC]

Hi guys,

I have a whole genome alignment for many species and a file containing coding sequence coordinates for one focal species, which I will use to extract 4d sites from the alignment and produce a phylogeny. What I would like to check is if what is a 4d site in the focal species actually corresponds in the alignment to 4d sites for each of the other species i.e. for each codon in the focal species which contains a 4d site, check each aligned codon for each species individually to ensure that they also have a 4d site at that position. Does anybody know of any existing software which can check this?

Cheers, Rory

[5heikki]

Can't you just extract all the 4d sites into a new alignment and then check it column by column with something like sort?

[RoryC]

Hi, thanks for the suggestion! I could see a way of writing a code for this, but I imagine it would be more complicated than that as you'd have to compare to a codon table to make sure the codon for each specific species has a 4d site in the 3rd position.

[haoyan14ioz]

Hi RoryC, I have the same question as you. Have you solved this problem? Could you share the script or software to me? Many thanks in advance.

Answer 1

[mtollis]

If your focal species is a reference species in your alignment as in one constructed with MULTIZ, and it has available CDS annotations, you should try msa_view from the PHAST package.

http://compgen.cshl.edu/phast/