phylofactor statistics

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Citations per year

Number of citations per year for the bioinformatics software tool phylofactor

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phylofactor specifications


Unique identifier OMICS_25257
Name phylofactor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data a “phylofactor” object which summarize, plot, cross-validate, run null simulations, and parse out the information from phylofactorization.
Operating system Unix/Linux
Programming languages C, R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Alex Washburne

Publication for phylofactor

phylofactor citation


Phylogenetic factorization of compositional data yields lineage level associations in microbiome datasets

PMCID: 5345826
PMID: 28289558
DOI: 10.7717/peerj.2969
call_split See protocol

[…] rmality properties for compositional data to allow the application of standard multivariate methods (), and the ILR transform serves as a measure of contrast between two groups. The log-ratio used in phylofactor is an averaged ratio of abundances of taxa on two sides of an edge (see for more detail), thus phylofactorization searches the tree for the edge which has the most predictable difference […]

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phylofactor institution(s)
Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA; Program for Computational Biology and Bioinformatics, Duke University, NC, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC, USA; Department of Computer Science, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Statistical Science, Mathematics, and Computer Science, Duke University, Durham, NC, USA
phylofactor funding source(s)
Supported by the Defense Advanced Research Projects Agency (DARPA; D16AP00113).

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