JPhyloIO is an open source Java library for reading and writing phylogenetic file formats. The main aim is to provide a library that allows access to various formats using a single interface, while being independent of the concrete application data model, to achieve maximal flexibility. It supports event based reading and writing of the following alignment and tree formats:
SETSblocks, as well as the
MIXEDdata type extension defined by MrBayes). In addition a Nexus API is offered that allows application developers to easily add support for additional (custom) blocks and commands.
Application developers are able to implement format-independent data processing by including event based readers from JPhyloIO via the abstract strategy pattern. All readers in JPhyloIO are designed to deal with large amounts of data (alignments with many and/or very long sequences, large trees) without using a great amount of resources (CPU or RAM).
Look at the Demo Applications to quickly get started and see the possibilities of JPhyloIO.
You can get an overview on how to use JPhyloIO in the documentation:
If you have any questions regarding JPhyloIO or want to use it with your code in the current status already, feel free to email to stoeverbioinfweb.info.
JPhyloIO is currently used in the following software: