Ortholog assembly and extraction

Question

[bagdiev39]

I am extracting ortholog genes from genome databases, where genes are not annotated. I have used blast to generate hits against the database using genes of fully annotated genomes. Currently I am using Geneious to map these hits against the genes and then extract the assembled gene (which will have several gaps) Is there a way to automate this process of mapping the hits to the respective gene in one go?

[GenoMax]

Many seem to use orthofinder for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder

[dthorbur]

I really like orthofinder and use it frequently, but there are also plenty of other tools out there. Here is a recent review with a few of the best tools and how they differ.