title: A format for phylogenetic placements.
abstract: We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.
authors.affiliation: Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America. matsen@fhcrc.org
authors.forename: Frederick A
authors.initials: FA
authors.lastname: Matsen
authors.forename: Noah G
authors.initials: NG
authors.lastname: Hoffman
authors.forename: Aaron
authors.initials: A
authors.lastname: Gallagher
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D016013:Likelihood Functions; D010802:Phylogeny; D011381:Programming Languages; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface