cogent3 2020.6.30a0

COmparative GENomics Toolkit 3

cogent3

cogent3 is a mature python library for analysis of genomic sequence data. We endeavour to provide a first-class experience within Jupyter notebooks, but the algorithms also support parallel execution on compute systems with 1000's of processors.

Who is it for?

Anyone who wants to analyse sequence divergence using robust statistical models

cogent3 is unique in providing numerous non-stationary Markov models for modelling sequence evolution, including codon models. cogent3 also includes an extensive collection of time-reversible models (again including novel codon models). We have done more than just invent these new methods, we have established the most robust algorithms for their implementation and their suitability for real data. Additionally, there are novel signal processing methods focussed on statistical estimation of integer period signals.

Anyone who wants to undertake exploratory genomic data analysis

Beyond our novel methods, cogent3 provides an extensive suite of capabilities for manipulating and analysing sequence data. You can manipulate sequences by their annotations, e.g.

Plus, you can read standard tabular and biological data formats, perform multiple sequence alignment using any cogent3 substitution models, phylogenetic reconstruction and tree manipulation, manipulation of tabular data, visualisation of phylogenies and much more.

Anyone looking for a functional programming style approach to genomic data analysis

Our cogent3.app module provides a very different approach to using the library capabilities. Notably, a functional programming style interface lowers the barrier to entry for using cogent3's advanced capabilities. It also supports building pipelines suitable for large-scale analysis. Individuals comfortable with R should find this interface pretty easy to use.

Installation?

$ pip install cogent3

Install extra -- adds visualisation support

NOTE: Only available in the development version until release ≥2020.3

The extra group includes python libraries required for visualisation (i.e. plotly and psutil plus pandas (optional)

$ pip install cogent3[extra]

Install dev -- adds cogent3 development related libraries

The dev group includes python libraries required for development of cogent3.

$ pip install cogent3[dev]

Install the development version

$ pip install git+https://github.com/cogent3/cogent3.git@develop#egg=cogent3

Project Information

cogent3 is released under the BSD-3 license, documentation for cogent3 is on readthedocs, while cogent3 code is on 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.

Project History

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 PyEvolve in 2004) and it's Python 3 only.

Given this history, we are grateful to the multitude of individuals who have made contributions over the years. These individuals are explicitly acknowledged in all the files they contributed to and were co-authors on the original PyEvolve and PyCogent publications.

Compared to PyCogent version 1.9, there has been a massive amount of changes. These include integration of many of the new developments on algorithms and modelling published by the Huttley lab over the last decade. We have also modernised our dependencies. For example, we now use plotly for visualisation, tqdm for progress bar display, concurrent.futures and mpi4py.futures for parallel process execution, tox and pytest for unit testing.