v1.0.0b2

Install

You can install the latest release using pip install OrthoEvol. It's available on pypi

What's Changed

• Quick fixes to update docs and modules by @sdhutchins in #129
• Update dev-master to master by @sdhutchins in #130
• Updated docstrings and documentation by @sdhutchins in #132
• Create PULL_REQUEST_TEMPLATE.md by @sdhutchins in #136
• Reformatted pal2nal.py and updated index.html by @sdhutchins in #137
• Updated package requirements and index.html by @sdhutchins in #138
• Update tablib version by @sdhutchins in #140
• Update dev-master to master by @sdhutchins in #141
• Created Readthedocs Yaml Configuration by @sdhutchins in #142
• WIP Merge Utilities Branch to DB_Mana_Patch by @grabear in #144
• Light refactoring of database management patch by @sdhutchins in #146
• Completion of working DatabaseManagement. by @grabear in #145
• Implement taxid-based blastn (#147) by @sdhutchins in #147
• Add missing attributes. by @sdhutchins in #151
• Add Tools/PBS module, a rework of the Tools/SGE module. by @grabear in #152
• Bump werkzeug from 0.12.1 to 0.15.3 in /OrthoEvol/Cookies/new_website/{{cookiecutter.website_name}}/requirements by @dependabot[bot] in #157
• Bump flask from 0.12.1 to 1.0 by @dependabot[bot] in #158
• Bump psutil from 5.2.2 to 5.6.6 by @dependabot[bot] in #161
• Bump flask from 0.12.1 to 1.0 in /OrthoEvol/Cookies/new_website/{{cookiecutter.website_name}}/requirements by @dependabot[bot] in #162
• Fix AttributeError by @sdhutchins in #165
• Add more module testing and upgrade to pytest by @sdhutchins in #166
• Migrate to pytest and implement code coverage. by @sdhutchins in #167
• Major updates to database management, ftp, pbs, etc. by @grabear in #155
• Release 1.0.0b2 by @sdhutchins in #213
• Bump flask from 1.0 to 2.2.5 in /OrthoEvol/Cookies/new_website/{{cookiecutter.website_name}}/requirements by @dependabot[bot] in #214
• Fix readthedocs build. by @sdhutchins in #215
• Add tests, Fix README by @sdhutchins in #216
• Add pyproject.toml by @sdhutchins in #217

Full Changelog: 0.9.0a2...1.0.0b2

OrthoEvolution

OrthoEvolution is an easy to use and comprehensive python package which aids in the analysis and visualization of comparative evolutionary genetics related projects.

Overview

This package is focused on the inference of orthologs using NCBI's blast, various sequence alignment strategies, and phylogenetics analyses including PAML, PhyML, ete3, and more tools.

Ultimately, the goal is to create a reusable pipeline for the inference of orthologs in order to ensure reproducibility of data as well as improve the management and analysis of (what can be) large datasets.
The Cookies, Manager, Pipeline, and Tools modules act as a framework for our workflow, while the Orthologs module provides access to specific functions for our various ortholog inference projects.

View our read the docs and feel free to also read this related paper to gain more insight into this project/python package.

Installation

View the below methiods for installing this package.

PyPi

pip install ortho-evol

GitHub

1. Download the zip file and unzip it or git clone https://github.com/datasnakes/OrthoEvolution.git
2. cd OrthoEvolution
3. pip install .

Development Code

WARNING : This code is actively under development and may not be reliable. Please create an issue for questions about development.

1. Download the zip file and unzip it or git clone -b dev-master https://github.com/datasnakes/OrthoEvolution.git
2. cd OrthoEvolution
3. pip install .

Examples

Check out this tutorial in our Wiki Docs.

import OrthoEvol

Tests

To run tests, type nosetests Tests/ in the OrthoEvolution directory.

Contributors

This package was created by the Datasnakes Team.

• Rob Gilmore | Github: @grabear | ✉
• Shaurita Hutchins | Github: @sdhutchins | ✉

If you would like to contribute to this package, install the package in development mode,
and check out our contributing guidelines <https://github.com/datasnakes/OrthoEvolution/blob/master/CONTRIBUTING.rst>__.

Citations

We're so thankful to have a resource such as `Biopython <http://biopython.org/wiki/Biopython>`__. They inspired this package.

*Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and Bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163
pmid:19304878*