Phylogenetic Analysis Based On Motif Alignment

Question

[Ripeapple]

Hello,

I've been struggling about constructing the phylogenetic tree based on multiple protein sequence alignment. There are two conserved domains in the protein, and we 'd like to give more penalty to the residue substitutions in two domains. Is there any program or script to do that? Any input appreciated, thanks a lot,

Answer 1

[Eric T.]

Yes, RAxML lets you specify an array of weights for each column in the alignment.

You can use GUIDANCE to create and/or validate your alignment, and the server also allows you to export a file with the estimanted conservation or reliability of each column in the alignment, for use with RAxML. GUIDANCE can also remove unsupported or poorly aligned columns from your alignment, which is a good idea.