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# JPhyloIO
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:
* [*NeXML*]( including its different types of metadata
* *Nexus* (including the `TAXA`, `DATA`, `CHARACTERS`, `UNALIGNED`, `TREES` and `SETS` blocks, as well as the `MIXED` data 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.
* *PhyloXML*
* *FASTA* (including support for *FASTA* comments and column indices)
* *Newick* tree format
10  * *Phylip*
11  * *Extended Phylip*
12  * *MEGA* (including different types character set definitions, reading only)
13  * *PDE* (the format of the alignment editor [*PhyDE*](, reading only)
14  * *XTG* (the format of the phylogenetic tree editor [*TreeGraph 2*](, reading only)
16  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).
18  *JPhyloIO* is distributed under [LGPL]( More information can be found at
20  ## Getting started
22  We have several [tutorials]( available that show how to use *JPhyloIO* for reading and writing phylogentic data step by step. Additionally the [general documentation]( provides and overview and contains a detailed [JavaDoc](
24  If you have further questions, feel free to ask one on our [ResearchGate project page]( or contact
26  ## Source code
28  This *GitHub* repository in a synchronized mirror of the [master repository at bioinfweb]( Feedback and pull requests are welcome. Synchronization was made possible by [*SubGit*](
30  ## Issues
32  If you want to submit a bug report or feature request, please use our public bug tracking system at (We do not manage issues on GitHub directly.)
34  ## License
36  The latest versions of *JPhyloIO* are distrubuted under [GNU General Lesser Public License Version 3]( See [NOTICE.txt]( for further details.
38  This product includes dependencies developed by the [Apache Software Foundation]( distributed under the terms of the [Apache License Version 2.0](
40  ## Binary releases
42  Binary releases and *Maven* code can be found at
44  ## About *bioinfweb*
46  * Legal notice:
47  * Privacy policy:

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