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Qiita - A multi-omics databasing effort
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
A very fast and scalable phylogenetic visualization viewer
exploratory and interactive microbiome analyses based on heatmaps
The website for the American Gut Project participant portal
Deblur is a greedy deconvolution algorithm based on known read error profiles.
Hierarchical orderings for mass spectrometry data
Emperor a tool for the analysis and visualization of large microbial ecology datasets
Automated taxonomy decoration onto a tree
QIIME2 plugin for fragment insertion
SortMeRNA: next-generation sequence filtering and alignment tool
Sample search by metadata and features
conda recipes for bioinformatic tools like blast+, infernal, etc.
A QIIME2 plugin for working with and processing American Gut data
compositional data analysis and visualization toolbox
Workflow for detecting genome-wide horizontal gene transfers
Code repository of the Earth Microbiome Project.
Multidimensional scaling algorithms for microbiology-ecology datasets.
A QIIME2 plugin for benchmarking high precision genome matching from amplicon data
descrete False Discovery Rate method
The Biological Observation Matrix (BIOM) Format Project
Microbial analysis in TCGA data
annotation pipeline for microbial genomes and metagenomes
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests
structural annotation pipeline for microbial genomes and metagenomes
Administration website for the Knight Lab