rnaimehaom / aspen

ASPEN repository, associated with 2019 publication

ASPEN

Summary

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.

Note about parallelization

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.

Requirements

Dependencies

ASPEN topology enumeration code runs under python 2.7 and requires the biopython package. The test suite additionally requires the mock package.

Input requirements

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.

Basic operation instructions

1. Make sure aspen is in the PYTHONPATH
2. Place pairwise path length distributions file in working directory
3. Call python -m aspen.run distributions file [number of processes]

Default number of processes to use for enumeration is 4.

License

ASPEN is published under the GNU General Public License as published by the Free Software Foundation, version 3 of the License. See license.txt