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,
An important component of our research is the development of new bioinformatic tools and resources to facilitate processing, analysis, and visualization of large data sets. Our software tools are available
Exploration of environmental and host-associated microbiota relies on robust, high-throughput molecular and microbiological techniques to produce high-quality reproducible data. To support our projects, there are on-going development efforts to establish
Microbes are ubiquitous and diverse, yet microbial communities exhibit repeatable patterns across many ecosystems and sample types. It is likely that some aspects of microbial ecology may be useful as
Microbes are the most diverse and abundant entities on Earth, and they are critical to ecological and biogeochemical processes such as decomposition, plant growth, and nutrient cycling. They also have
Like humans, animals are hosts to vast microbial communities. Describing animal-associated microbiota allows us to detect similarities and differences to the human-associated microbiota which facilitates a better understanding of human
The human body harbors an estimated ten times as many microbial cells as human cells. By studying these microbes, we can learn more about ourselves, as microbial communities may record
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
