This work is supported in part by a National Science Foundation grant (CCF-0622037), a Department of Energy grant (DE-FG02-06ER25734), and grant R01LM009494 from the National Library of Medicine. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the DOE, NSF, National Library of Medicine or the National Institutes of Health.
NEPAL is developed entirely in C++. To obtain a copy of the tool, download the most recent version from the link below; currently, we provide only a linux executable. Usage instructions can be found in the User Documentation associated with the release downloaded. Unfortunately, we lost access to the source code of the tool, which means we can't fix any bugs/problems with the current executable. We're in the process of rewriting the tool.
Check out the PhyloNet tool for tree comparison-based tools for phylogenetic network reconstruction.