Title |
A Format for Phylogenetic Placements
|
---|---|
Published in |
PLOS ONE, February 2012
|
DOI | 10.1371/journal.pone.0031009 |
Pubmed ID | |
Authors |
Frederick A. Matsen, Noah G. Hoffman, Aaron Gallagher, Alexandros Stamatakis |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 6 | 55% |
United Kingdom | 2 | 18% |
Germany | 1 | 9% |
Egypt | 1 | 9% |
Unknown | 1 | 9% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 9 | 82% |
Members of the public | 2 | 18% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 3% |
Netherlands | 1 | <1% |
Australia | 1 | <1% |
Brazil | 1 | <1% |
Germany | 1 | <1% |
Canada | 1 | <1% |
Sweden | 1 | <1% |
Spain | 1 | <1% |
Denmark | 1 | <1% |
Other | 0 | 0% |
Unknown | 132 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 40 | 28% |
Researcher | 32 | 22% |
Student > Master | 17 | 12% |
Student > Bachelor | 16 | 11% |
Student > Doctoral Student | 9 | 6% |
Other | 18 | 13% |
Unknown | 12 | 8% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 72 | 50% |
Biochemistry, Genetics and Molecular Biology | 21 | 15% |
Computer Science | 12 | 8% |
Environmental Science | 6 | 4% |
Immunology and Microbiology | 4 | 3% |
Other | 11 | 8% |
Unknown | 18 | 13% |