Summary: BuddySuite is a collection of four independent yet interrelated command-line programs that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction. Common sequence, alignment, and tree file formats are automatically detected and parsed, and nearly 100 routine tasks have been combined into this comprehensive suite of toolkits. Availability and Implementation: The project has been implemented in Python 3 for use on UNIX-based systems. Installation is performed using a dedicated graphical installer or by cloning the development Git repository. All source code is freely available. Home page: http://research.nhgri.nih.gov/software/BuddySuite Contact: andy@mail.nih.gov, steve.bond@nih.gov Supplementary information: Complete documentation for each tool in the BuddySuite is available at http://tiny.cc/buddysuite_wiki