Pyvolve

Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. Please ensure you are using the most up-to-date version of Pyvolve! The current version is 1.1.0.

A detailed user manual for Pyvolve is available here, and API documentation for Pyvolve is available at https://sjspielman.github.io/pyvolve.

Pyvolve has several dependencies:

• Biopython
• Scipy and Numpy (with Numpy >= 1.7)

Currently, pyvolve development is occurring in Python3.x with absolutely no plans to return to Python2. The following examples therefore assume Python3 (which you may have on your computer named as python3 and not python!)

You can install Pyvolve directly using pip or easy_install (note that, if needed, these lines will install any missing dependencies for you!):

pip install pyvolve
# OR
easy_install install pyvolve

Note that these commands might need sudo in front, depending on your permissions.

To update your version of Pyvolve (for pip), simply use the --upgrade argument (again, possibly w/ sudo):

pip install --upgrade pyvolve

Alternatively, you can download and install from source. Download the most recent version of Pyvolve from the Releases tab (https://github.com/sjspielman/pyvolve/releases), uncompress the file, and navigate into the pyvolve/ directory. From this directory, enter the following commands:

sudo python setup.py install
sudo python setup.py test  # optional, but recommended!

If you do not have root privileges, you can install Pyvolve for only you (the user!) with this line instead:

python setup.py install --user

Please file any bugs and/or relay any questions under the Issues tab: https://github.com/sjspielman/pyvolve/issues.

If you use Pyvolve in your research, please cite the following:
Spielman, SJ and Wilke, CO. 2015. Pyvolve: A flexible Python module for simulating sequences along phylogenies. PLOS ONE. 10(9): e0139047.

@article{SpielmanWilke2015,
author = {Spielman, S. J. and Wilke, C. O.},
title = {Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies},
journal = {PLOS ONE},
year = {2015},
volume = 10,
pages = {e0139047}
}