phylogeo

The software tool 'phylogeo' is an R package that provides geographic utilities for sequencing-based microbial ecology studies. It offers a set of plotting and mapping functions to visualize the geographic distribution of samples, look at the relatedness of microbiomes using ecological distance, and map the geographic distribution of particular sequences. It extends the popular phyloseq package and uses the same data structures and command formats, making it easy to map and explore the geographic dimensions of data from the R programming language.

Topic

Microbiology;Microbial ecology;Phylogenetics

Detail

  • Operation: Visualisation

  • Software interface: Command-line user interface

  • Language: R

  • License: Not stated

  • Cost: Free

  • Version name: -

  • Credit: National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: Zachary Charlop-Powers zcharlop@rockefeller.edu

  • Collection: -

  • Maturity: -

Publications

  • phylogeo: an R package for geographic analysis and visualization of microbiome data.
  • Charlop-Powers Z and Brady SF. phylogeo: an R package for geographic analysis and visualization of microbiome data. phylogeo: an R package for geographic analysis and visualization of microbiome data. 2015; 31:2909-11. doi: 10.1093/bioinformatics/btv269
  • https://doi.org/10.1093/bioinformatics/btv269
  • PMID: 25913208
  • PMC: PMC4547612

Download and documentation

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