Welcome to PyCogent3’s documentation!

Contents

WARNING & DISCLAIMER

Be warned that PyCogent3 is a significantly changed library from the original PyCogent. Most of these changes involve elimination of modules, conversion to PEP8 compliance and other refactors. These changes are still underway!

Please see the wiki pages for a detailed changelog on the API changes.

YOU CAN HELP!

Posting Bugs

If you discover a bug, especially something that worked in PyCogent but not in PyCogent3, please post a ticket!

When posting a ticket, please provide a minimum working example to reproduce the issue. Also include the versions of the library and other tools (e.g. attach the result of $ pip freeze > libs.txt).

Getting Involved

We would greatly appreciate assistance in updating the project to PEP8, or anything else you think needs doing.

Please post a ticket, or comment on an existing one, indicating your intention so we can assist. Then it’s the usual “fork”, “pull request” dance.

Overview

PyCogent3 is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.

Our primary goal is to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets.

Support

We acknowledge the provision by Wingware of free licenses for their professional IDE. Their committment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port of PyCogent to Python 3 was made much easier by using Wing’s refactor tools!)

Citation

If you use this software for published work please cite – Knight et al., 2007, Genome Biol, 8, R171.

Support

We acknowledge the provision by Wingware of free licenses for their professional IDE. Their committment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port of PyCogent to Python 3 was made much easier by using Wing’s refactor tools!)

News and Announcements

PyCogent3 News and Announcements are available via the News and Announcements Blog at http://pycogent.wordpress.com.

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