2.9 years ago by
You can make such files easily with one of the many MSA online apps: https://www.ebi.ac.uk/Tools/msa/
Simply choose sequences of homologs from different species of interest and try the different tools. That way you can also compare the effect of different MSA algorithms and parameters on the resulting phylogenies.
Another quick way is to use TreeFam, that way you can save yourself some work, you do not need to pick homologues yourself. Use a single sequence of interest or press the Example button, then for inserting the sequence into the tree, TreeFam will calculate a MAFFT alignment which you can also download.