This repository contains scripts used to design target loci from transcriptome sequence. It assumes that you have identified homologous sequence between multiple species, and the starting input is a directory with one fasta alignment for each locus (each alignment should have 2-3 individuals).
If you want to design probes that target a single exon per locus, rather than tiling across all exons in a transcript, see my other repo on Plethodon probe design