mutpath is a Python package for identifying mutational paths through sequence space generated using the MarkovJumps feature of BEAST.
This package was created by Jesse Bloom. It is based on the approach used to generate the mutation trajectories in Gong et al, 2013. The mutation-mapping BEAST itself was implemented by Marc Suchard. It can be used to create mutational paths similar to that in Figure 2A of Gong et al, 2013.
mutpath source code is available on GitHub. You can download a ZIP file of the repository from this site by clicking on the Download ZIP button on the right side.
mutpath documentation is available on GitHub Pages.
If you use mutpath, please cite Gong et al, 2013 as the reference describing the approach.
This package contains a number of scripts that interface with BEAST. These scripts generate mutational trajectories through sequence space and other associated data from BEAST output. Briefly, BEAST is used to sample phylogenetic trees with mutations mapped to branches from the posterior distribution. These trees make it possible to calculate the posterior probability for different trajectories through sequence space between two known sequences.
Some example analyses are included in the ./examples/ subdirectory of the main package repository.