Autophy is a Python module that provides objects and methods for organizing and simplifying manipulation of PHLAWD alignments through the use of a SQLite database structure. Included scripts provide methods to import multiple individual PHLAWD alignments into a SQLite database where sequences are indexed by taxonomy, and to query such a database in order to generate concatenated alignment files in phylip format, which are usable by RAxML as well as other phylogenetics software.
Autophy is still in development.