Tools for comparative analysis of eukaryotic genomic sequences


I have got multiple FASTA files (each represents a section of the chromosome of a eukaryotic). I also have gene annotation (gff3 format) downloaded from NCBI data viewer.

My aim is to find the genes/regions which are common across the multiple fasta files. The task would also involve finding Repeats, Orthologues, paralogues e.t.c.

Any suggestion for bioinformatics tools for this task? Is there some tool in Galaxy for this?

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