I have a protein alignment, I translate it to CDS alignment using pal2nal.pl, after using Gblocks with -t=c to remove the gaps, I translated it back to protein alignment, however, it's not consistent with the original protein anymore.
The CDS alignment is in attachment, if you are interested, please have a try.
Sincerely,
Kang
I guess it should be like that. The translation works good in one direction but when you do reverse translation, you will not get the same result. I think it is obvious thing and due to degeneracy of code. Additionally, you have trimmed some information by Gblocks.
So, its not a bug, it is just that the method you are using is not correct.
Abhijeet Singh thank you for your join-in and suggestions. My understanding was that, for a codon alignment, during removing gaps using Gblocks -t=c, when a site need to be removed, the codon containing the site would be removed as a whole. then we could have a result alignment which is also a codon alignment. So I was wrong?
I don't understand what you mean. But Gblock just removes the part of an alignment which does not provides much information to the phylogenetic interpretation or tree building. Even, the use of trimming software like Gblocks or trimAl is debatable. Some use it while some do not. So I don't understand what you mean by -t=c.
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