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Table 1 Formats supported by JPhyloIO

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

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  
phyloXML XML    X X X X 3 X X
MEGA Text   X       X  
PDE XML   X    X    X  
XTG XML    X   X    X  
  1. 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
  2. 1Attaching simple numeric or textual values to data elements
  3. 2Attaching complex metadata elements that may be represented as XML structures
  4. 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