How to select multiple domains from protein sequences to align them and build a phylogenetic tree

Question

[Michela]

Hi everyone of Biostars community!

I have a bunch of protein sequences that I have aligned with the multiple sequence alignment tool MUSCLE, as next step I would like to extract the sequences of the conserved domains from the alignment in order to aligned only them and build a phylogenetic tree out of it.

I may do it manually I guess by using SeaView (MSA viewer tool) to edit the alignment and copy-paste the domain from each sequence, but I was wondering if there is a faster way since I have 71 sequences aligned, each with 3/4 domains to extract.

I have seen in other posts the existence of Gblock but I'm not able to run even to open the example file (it gives me the error 'file can't be opened')

Thank you in advance for the help, Michela :)