Bioinformatics Research Guide: Clustal Omega

Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. 

Clustal omega Help and documentation:

https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Clustal+Omega+Help+and+Documentation