Concatenate multiple MUSCLE alignment result to build a phylogenetic tree

Question

[huiyus97]

Hi,

I want to build a phylogenetic tree based on single copy orthologous proteins which I got using OrthoMCL. I aligned each protein group using MUSCLE separately and I want to concatenate those proteins to build a phylogenetic tree using RAXmL. Could someone please recommend me some tools which I can use to concatenate those protein sequences, or can I do it with RAXmL?

Thank you so much for your help!

[h.mon]

Plenty of methods here:

How to concatenate multiple fasta file

Answer 1

[Mensur Dlakic]

This script works well. I suggest you trim the alignments before concatenation - see here and here.