baitfindR is an R package that extends the Yang and Smith orthology inference pipeline (2014 Mol. Biol. Evol. 31:3081-3092) to find appropriate loci for use as baits in sequence capture.
You can install baitfindR as follows:
install.packages("devtools")
devtools::install_github("joelnitta/baitfindR")Most functions are wrappers for other external (to R) programs, so these must be installed and on the users' PATH. baitfindR requires all of the dependencies for the Yang & Smith workflow.
A docker image is available that includes the latest version of baitfindR and all required, properly versioned dependencies.
baitfindR works best in conjunction with drake to manage a bait-finding workflow. Please see the example project.