I'm trying to find orthologs and lineage specific paralogs between two species. I tried using the ensembl homology pipeline but both my species are not on the database. Therefore, I tried to write my own similar pipeline. So far I've accomplished the following:
1. Blast all for every gene in both genomes
2. Filtering of blast results based of evalue and alignment length
3. Single Linkage clustering with MCL to form gene families
4. For each gene family, I did a protein alignment with PRANK and built a tree with Treebest, which also takes in the species trees and tries to build a gene tree accordingly.
My question deals with parsing these gene trees. I want to use these gene trees to find paralogs and orthologs between my two species but I'm not sure how to parse all of the topologies of these trees and how to determine paralogous or orthologous relationships.
Are there any programs that can take in gene trees and output a list of paralogs and orthologs?