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Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

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Emperor a tool for the analysis and visualization of large microbial ecology datasets

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American Gut open-access data and IPython notebooks

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The Biological Observation Matrix (BIOM) Format Project

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exploratory and interactive microbiome analyses based on heatmaps

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Deblur is a greedy deconvolution algorithm based on known read error profiles.

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Robust Aitchison PCA from sparse count data

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Code repository of the Earth Microbiome Project.

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A fast and scalable phylogenetic tree viewer for microbiome data analysis

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Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse...

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