Knight Lab, University of California

As microbial ecologists continue to take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic


Evident is a web-based software tool with an interactive user interface, implemented in HTML, Web Graphics Library, mod_python and QIIME. The interface of Evident provides: (i) parameter selection (i.e., study


EMPeror is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets. Due to its tailor-made graphical user interface, delving into a new


QIIME (pronounced “chime”) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing


Qiita (canonically pronounced cheetah) is the QIIME database effort to enable rapid analysis of microbial ecology datasets. The Qiita repository is responsible for defining the data model and the Python


tax2tree is a tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. McDonald D,


Scikit-bio began from code derived from PyCogent, and the contributors and/or copyright holders have agreed to make the code they wrote for PyCogent available under the BSD license. The contributors to


PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of

Platypus Conquistador

Platypus Conquistador is a bioinformatics command line tool for the confirmation of the presence/absence of a specific taxon (or set of taxa) in environmental shotgun sequence reads. Platypus uses two


TopiaryExplorer supports visualization of very large trees while providing convenient interfaces for decorating the tree with taxonomic information, automatically coloring branches based on data about environments where they are observed,


BayesFold is a web application that finds, ranks, and draws the likeliest structures for a sequence alignment. Foldings are based on the predictions of the Bayesian statistical method. BayesFold provides


Primer Prospector is a pipeline of programs to design and analyze PCR primers. De novo primers can be generated from a set of aligned fasta sequences and these primers, or