Looking for any suggestions on the currently accepted methodology for isolating orthologous proteins from multiple datasets. We are working with eukaryotes who are non-model organisms. Our datasets are in proteins assembled using transdecoder and we have done our best to eliminate redundant sequences. I am somewhat familiar with Hamstr, Orthofinder, OrthoDB, etc. but am not super confident as to which method would be best. Our goal is to rule out paralogous genes and construct a phylogenetic tree. We then want to explore certain genes of interest that are shared between the different species. Any links to good reviews would also be appreciated.