JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface

Table 1 Formats supported by JPhyloIO

Format	Type	OTUs	MSAs	Trees	Networks	Simple Metadata¹	Complex metadata²	Ontologies³	Read	Write
FASTA	Text		X						X	X
PHYLIP	Text		X						X	X
Relaxed PHYLIP	Text		X						X	X
NEXUS	Text	X	X	X		X			X	X
Newick	Text			X		X			X	X
eNewick (Newick, NEXUS)	Text			X	X	X			X
NeXML	XML	X	X	X	X	X	X	X	X	X
phyloXML	XML			X	X	X	X	3	X	X
MEGA	Text		X						X
PDE	XML		X			X			X
XTG	XML			X		X			X

A variety of file formats used in phylogenetics are supported. These can either be based on XML, or define custom types of structured text which is indicated in the second column. The central columns show whether a format supports taxon/OTU lists, multiple sequence alignments, phylogenetic trees or networks and what type of metadata can be attached to at least some of these elements or their subelements. As shown in the two rightmost columns, JPhyloIO can read and write many of the common formats, while formats specific to single applications can only be read
¹Attaching simple numeric or textual values to data elements
²Attaching complex metadata elements that may be represented as XML structures
³Simple annotations can be linked using CURIE-like identifiers and custom XML tags can be added to all elements but no explicit reference to external ontologies is currently supported in phyloXML

ISSN: 1471-2105