JPhyloIO - A Java library for event-based reading and writing of different alignment and tree formats through one common interface

Stöver BC, Wiechers S, Müller KF

Zusammenfassung

Today a variety of alignment and tree file formats exist, some of which well-established but limited in their data model, others more recently proposed offer advanced future-orientated features for metadata representation. Most phylogenetic and other bioinformatic software currently only supports one or few different formats, while supporting many widely-used standards simultaneously would be desirable to achieve optimal interoperability and prevent data loss by external conversions. We developed JPhyloIO, which allows reading and writing of alignment and tree formats (NeXML, PhyloXML, Nexus, Newick, FASTA, Phylip, MEGA, XTG, PDE) using a common interface. It is the only currently available Java-library that generalizes between the different data and metadata concepts of all formats, while still allowing access to their individual features. By simply implementing a single JPhyloIO based reader and writer, application developers can easily support all formats in one step and the event-based architecture allows the library to be combined with any application business model design, while still being memory efficient for large datasets. We provide JPhyloIO as a service to the scientific community, which will benefit from simplified development of software that supports various standards simultaneously. Our aims are to increase the interoperability between different (phylogenetic) software tools and to foster usage of more recently proposed formats providing a powerful metadata concept. It currently integrated in a number of applications and is fully interoperable with our Java-library LibrAlign, which offers powerful components for multiple sequence alignments and attached raw and metadata. Download and documentation: http://bioinfweb.info/JPhyloIO/ .