Core genome Identification

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genetic_saint's picture
Core genome Identification

I'm trying to identify the core genome(genes which are common in all species) taking 10 species using reciprocal blast hits.I have formatted a blast database taking each species for the BLAST.However I'm selecting the first top hit from the results but  I'm getting redundancy in a way that sometimes query sequence have more then one hit from  the reference database .As core genome is supposed to be the collection of orthologous genes then which gene to select if the query have more then one hit.
Also how to compare this huge results(45 blast results) and find the common genes from the obtained blast results.Any solution is appreciated with regard to identifying Core genome using resiprocal blast hits