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Software |
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Since we're a lab focused on the computational side of biology, we have several bioinformatics software packages that we've either developed directly in our lab or in conjunction with other bioinformatics labs.
QIIME (Quantitative Insights Into Microbial Ecology) is an open source software package for the comparison and analysis of microbial communities, taking users from their raw sequencing data through publication-quality graphics.
PyCogent (Python COmparative GENomic Toolkit) is an open source software library that provides a wide variety of functionality for the manipulation and analysis of genome biology data sets.
The BIOM Format (BIological Observation Matrix Format) is a JSON-based file format for storing general sample by observation contingency tables. In addition to the format itself, an API is provided in multiple programming languages to support the use of the format in bioinformatics software.
PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.