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.
Version 4.01. Available modules:
module add jane-4.01 jane-cli.sh -h
Free for MetaCentrum users