I have completed finding ortholog proteins (proteome data) of 16 species by using orthoMCL tool. After that, I want to make a phylogenetic tree based on orthologs proteins among those species. Could you please help how to do that? For instance, I have IDs of orthologs and how can I get related proteins from my own protein data (in orthoMCL output)? and use them for the phylogenetic tree?
Thank you for taking a time.