A month ago, I asked a question on how to detect paralog sequences in target enrichment when single-copy genes are NOT known: Paralog detection after target capture - HybPiper. A user replied that a de novo assembler such as SPAdes (which is used in HybPiper; a pipeline to extract target sequences from raw reads) would potentially collapse paralogs.
In order to face this problem, someone else suggested me to retrieve complete genomes that are similar enough to my non-model species and build a list of single-copy genes (there are less than 10 available genomes that I could use). Then assume that those genes are also single-copy in my species of interest.
So the question is: how to identify single-copy genes across multiple complete genomes?