Welcome to Cogent3’s documentation!

COGENT3 IS HEADING TO A NEW HOME!

We will be leaving Bitbucket and heading to GitHub soon. All issues will be migrated over to the new home. Rest assured, any issues to you post at issues will not be lost.

Contents

Note

All the code presented in this documentation is working, but does not reflect the current best-practice. The documentation will be significantly revised in the next couple of months.

WARNING & DISCLAIMER

Be warned that Cogent3 is a significantly changed library from the original PyCogent. The renaming has been done to emphasise these differences and to make the project name and import statement consistent (cogent was always the import name, originating in the pyevolve project from 2004!).

Most of the changes from PyCogent involved elimination of modules, using black and isort for coding style, rationalisation of interfaces and the addition of new features. For instance, we have an experimental cogent3.app module (documentation still being written) that is intended to present a functional programming style interface to cogent3 capabilities.

The rewrite has been a massive amount of work and unfortunately the changes to the API are only partially documented at present – please see the wiki pages. We will endeavour to make that up-to-date when we can. But if you want to see what happened to something, search in the repository history.

YOU CAN HELP!

Posting Bugs

If you discover a bug please post a ticket at the issues page!

Overview

Cogent3 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 rigorously 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 commitment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port 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 commitment, 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!)