Hello, I have about 100 genomes (in fasta format) of a species of yeast

I also downloaded the reference genome assembly and the annotation file (in gff3 format), protein and transcript are also available

I know how to call SNPs, but if it is possible to analyze my data with orthologous genes (there are 5,000 genes listed in gff file)?

I have no idea how or which pipeline to use to get the homologous genes of all samples from the gff file

thanks for any suggestions!