We welcome all code contributions, from helping to improve the code, fix bugs, improve usability, and improve documentation, which is rather sparse, at the moment.
Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.
Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across amniotes. We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting.
We have several larger probes sets in the works for fishes, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. You can now buy this probe set direct from MYcroarray in the form of a capture kit.
Many of the steps, at this point, require that you are comfortable working with computer software on the command line. MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.