Just wondering - after assembling my reads to a reference protein-coding sequence for a bunch of genes, I happened to notice that for a couple certain clades I just did not get any sequence from them.
Is this a case of a gene being lost in the clade, or are their particular sequences too divergent to be mapped to my reference? Is there a way to tell? I wlll also mention some random other species missing the gene (no sequence obtained) but nothing as consistent as from a whole clade. This was from target exon capture.