After we collected hundreds of one-copy orthologs among tens of specices, we want to generate a phylogenetic tree. But for the alignments of those sequences we are not sure what is the canonical steps?
(1) Should we concatenate protein or DNA sequences in each species then do the multiple alignment? Or should we do the multiple alignment for each ortholog and then concatenate the alignments of each orthologs? (2) Should DNA sequences be used or protein sequences? (3) What is the strategy to manually edit the alignments? Should the region showing a gap in any species be removed?