Topology reconstruction by enumeration using branch-and-bound, as described in the 2019 publication:
Sloutsky, R., & Naegle, K. M. (2019). ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models. ELife, 8. doi:10.7554/eLife.47676.
Although in some cases enumeration can be done effectively on one core, this code is set up for parallel reconstruction. Because there is some overhead to setting up the parallelization framework, this code actually runs less efficiently on one core. We recommend using at least 4 worker processes to take full advantage of the parallelization.
ASPEN topology enumeration code runs under python 2.7 and requires the biopython package.
The test suite additionally requires the mock package.
A file containing pairwise path length distributions (histograms) between each pair of leaves to be incorporated into reconstructed topologies.
Examples of path length distributions with short enumeration run times are provided.
- Make sure
aspenis in the PYTHONPATH - Place pairwise path length distributions file in working directory
- Call
python -m aspen.rundistributions file[number of processes]
Default number of processes to use for enumeration is 4.
ASPEN is published under the GNU General Public License as published by the Free Software Foundation, version 3 of the License. See license.txt