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 v0.9.0.
A detailed user manual for Pyvolve is available here, and API documentation for Pyvolve is available at http://sjspielman.org/pyvolve.
Pyvolve has several dependencies:
- Biopython
- Scipy and Numpy (with Numpy >= 1.7)
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 pyvolveNote 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 pyvolveAlternatively, 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. Tests implemented **for Python2 only**If you do not have root privileges, you can install Pyvolve for only you (the user!) with this line instead:
python setup.py install --userPlease file any bugs and/or relay any questions under the Issues tab: https://github.com/sjspielman/pyvolve/issues.
Note that pyvolve itself is implemented for both Python2 and Python3, although its tests (python setup.py test) are implemented for Python2 specifically.
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}
}