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TreeBASE is a database and web front end that stores phylogenetic trees and the data matrices used to generate them. The current iteration comprises a complete rewrite of the schema and web layer, and will include a web services layer.
mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.