The diversification of homeobox genes is of great interest to evolutionary and developmental biology. To generate a catalogue of all homeobox genes within species of interest, it is necessary to sequence complete genomes. It is now possible for small research projects and individual laboratories to determine near-complete genome sequences of animal species. We provide bioinformatic methods for assembling draft genome sequences from any animal species, including read filtering and error correction, plus methods for extracting and classifying all homeobox sequences.