Jane
Description
Jane is a software tool for the cophylogeny reconstruction problem. The input to Jane is a file containing a "host" tree, a "parasite" tree, and a mapping of the tips of the parasite tree to tips of the host tree. The user may specify the costs of each of five types of events: cospeciation, duplication, duplication with host switch, loss, and failure to diverge. Jane then endeavors to find least cost mappings of the parasite tree onto the host tree subject to the given tip mapping. Note that while this documentation refers to the trees as "host" and "parasite," Jane is also used to reconcile other pairs of trees such as species trees and gene trees.
License
Free for MetaCentrum users
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of jane and load default version of jane as
module avail jane/ # list available modules module load jane # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail jane
and choose explicit version you want to use. Then run as
jane-cli.sh -h
Documentation
https://www.cs.hmc.edu/~hadas/jane/tutorial.html#CLI