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phyloacc / PhyloAcc

PhyloAcc a software to detect the changes of conservation of a genomic region
GNU General Public License v3.0
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Can PhyloAcc be used to analyse coding sequence alignments? #26

Closed KyleEwart closed 2 years ago

KyleEwart commented 2 years ago

Hi @ xyz111131, Can PhyloAcc be used to investigate accelerated evolution of a set of candidate genes (i.e. can the set of conserved elements be ‘coding’ genes)? Or is the program only suitable for conserved noncoding elements?

I was hoping to use PhyloAcc investigate rate changes for thousands of single-copy Orthologue protein sequences from ~10 species. If this is possible, could the input fasta file be an amino acid alignment, or would you suggest using the corresponding cds sequence alignments?

Many thanks in advance, Kyle

xyz111131 commented 2 years ago

Thanks for the question. The program is ideally for noncoding elements. Currently PhyloAcc doesn't support protein sequences as input. You could give CDS sequence a try, but PhyloAcc won't distinguish between synonymous and nonsynonymous substitutions.

KyleEwart commented 2 years ago

Thanks for the question. The program is ideally for noncoding elements. Currently PhyloAcc doesn't support protein sequences as input. You could give CDS sequence a try, but PhyloAcc won't distinguish between synonymous and nonsynonymous substitutions.

Many thanks for your reply. Regards, Kyle