cogent3 is a python library for genomic data analysis, specifically comparative genomics data.
We will be up on PyPI as soon as the documentation is written, until then it's download a tarball and pip install from that, or clone.
cogent3 is released under the BSD-3 license, documentation for cogent3 is on readthedocs, while cogent3 code is GitHub. If you would like to contribute (and we hope you do!), we have created a companion c3dev GitHub repo which provides details on how to contribute and some useful tools for doing so.
cogent3 is a descendant of PyCogent. While there is much in common with PyCogent, the amount of change has been substantial, motivating a new name cogent3. This name has been chosen because cogent was always the import name (dating back to 2004!) and it's Python 3 only.
Compared to PyCogent version 1.9, there have been a massive amount of changes. These include integration of many of the new developments on modelling of non-stationary processes published by the Huttley lab over the last decade. We have also modernised some convenience capabilities. For example, we now use tqdm for progress bar display and concurrent.futures and mpi4py.futures for parallel process execution.
We have implemented a cogent3.app module which contains a very different approach to using the capabilities. Notably, a functional programming style interface lowers the barrier to entry for using cogent3's advanced capabilities. Documentation is coming...
Importantly, the app interface should be considered as alpha level code.
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