I am very much a novice in bioinformatics and was wondering whether anyone might have any advice. I would like to extract areas of homology within a bunch of virus genomes, and then cut and funnel these sequences into a new file. Is this possible? Does anyone have any recommendations of any tools I could use to do this?

Lets say I have 10 distantly related retroviruses, I want to extract the areas of similarity and make a retrovirus 'metagenome', such that aligning small reads to this genome first, and then to the individual genomes would prevent my small read aligner from mapping to multiple virus genomes giving ambiguous results. I hope this makes sense. Any guidance anyone can give would be greatly appreciated.