Based on the assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes. Genefisher 2 is an interactive web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term "gene fishing" refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA.

BatCons2 is a tool for Backtranslation of aminoacid-sequences to nucleicacid-sequences and for ambiguos consensus sequence calculation based on a given alignment.