Given a set of genes in a FASTA-formatted file, for example:
exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an order of organisms, for example: Orthoptera?
BLAST is an obvious option, but I am not sure that it is the most efficient way considering there are likely thousands of organisms in that order. OrthoFinder also comes across as a valid option, but I am not sure how to implement such a thing considering the required inputs.
Any advice would be greatly appreciated!