Research software

  • QIIME, The Quantitative Insights into Microbial Ecology, a widely used package for the investigation of microbial community data. (pub)

  • BIOM, The Biological Observation Matrix, a candidate file format and API with the Genomic Standards Consortium for representing -omics data. (pub)

  • pyqi, An API to abstract business logic from interfaces.

  • scikit-bio, A BSD-licensed set of core objects, functions and statistics for working with biological data in Python

  • PICRUSt, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States used to predict metagenomic (and other) annotation profiles from 16S data. (pub)

  • tax2tree, A tool to automatically decorate a taxonomy onto a phylogenetic tree. (pub)

  • PyCogent, A toolkit to make sense from sequence. (pub)

…and the random