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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*](https://github.com/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*](https://github.com/NBISweden/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*](http://phyde.de/), reading only)
14  * *XTG* (the format of the phylogenetic tree editor [*TreeGraph 2*](http://treegraph.bioinfweb.info/), reading only)
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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).
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18  *JPhyloIO* is distributed under [LGPL](http://bioinfweb.info/JPhyloIO/License/LGPL). More information can be found at http://bioinfweb.info/JPhyloIO/.
19 
20  ## Getting started
21 
22  We have several [tutorials](http://r.bioinfweb.info/JPIODemo) available that show how to use *JPhyloIO* for reading and writing phylogentic data step by step. Additionally the [general documentation](http://bioinfweb.info/JPhyloIO/Documentation) provides and overview and contains a detailed [JavaDoc](http://bioinfweb.info/JPhyloIO/Documentation/API/Latest/).
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24  If you have further questions, feel free to ask one on our [ResearchGate project page](http://r.bioinfweb.info/RGJPhyloIO) or contact support@bioinfweb.info.
25 
26  ## Source code
27 
28  This *GitHub* repository in a synchronized mirror of the [master repository at bioinfweb](http://bioinfweb.info/Code/sventon/repos/JPhyloIO/list/). Feedback and pull requests are welcome. Synchronization was made possible by [*SubGit*](https://subgit.com/).
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30  ## Issues
31 
32  If you want to submit a bug report or feature request, please use our public bug tracking system at http://bioinfweb.info/JPhyloIO/Bugs. (We do not manage issues on GitHub directly.)
33 
34  ## License
35 
36  The latest versions of *JPhyloIO* are distrubuted under [GNU General Lesser Public License Version 3](http://bioinfweb.info/JPhyloIO/License/LGPL). See [NOTICE.txt](https://github.com/bioinfweb/JPhyloIO/blob/master/main/info.bioinfweb.jphyloio.core/src/NOTICE.txt) for further details.
37 
38  This product includes dependencies developed by the [Apache Software Foundation](http://www.apache.org/) distributed under the terms of the [Apache License Version 2.0](https://github.com/bioinfweb/JPhyloIO/blob/master/main/info.bioinfweb.jphyloio.core/src/APACHE-LICENSE.txt).
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40  ## Binary releases
41 
42  Binary releases and *Maven* code can be found at http://bioinfweb.info/JPhyloIO/Download.
43 
44  ## About *bioinfweb*
45 
46  * Legal notice: http://bioinfweb.info/About
47  * Privacy policy: http://bioinfweb.info/Privacy


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