So I am attempting to find covariance and long story short I am attempting a 28waymultiZ vertebrate MAF file as my input, but I need to remove any of the species that have an excessive number of gaps (or almost all gaps for any given maf block). Is there anyway to do this in a text maniuplation? I know, for example, when you stitch maf blocks you can select which species to keep, would that work without a bed file to designate the range? Or could I use a bed file that designates the entire range or would that mess it up somehow? I'm at a loss, but ultimately I need to remove some species from my MAF file so I have better allignment in the remaining species. Thanks again!