mutpath is a Python package for identifying mutational paths through sequence space generated using the MarkovJumps feature of BEAST.
mutpath source code is available on GitHub at https://github.com/jbloom/mutpath
mutpath documentation is available at http://jbloom.github.com/mutpath/
mutpath was written by Jesse Bloom. It takes advantage of the MarkovJumps feature added to BEAST by Marc Suchard.
If you use this software package, please cite the following reference for mutpath's approach to building mutational paths: Gong et al, 2013.
mutpath is free software under the GPLv3 license.
Specific examples of usage included in this package:
- A description of how to build mutational paths similar to that in Figure 2A of Gong et al, 2013 can be found at http://jbloom.github.io/mutpath/example_influenza_human_H3N2_NP.html
- A description of the process used to build the mutational paths in Gong and Bloom, 2014 is at http://jbloom.github.io/mutpath/example_influenza_NP_1918_Descended.html