Jane tree file generator
========================

Version 0.4
Daniel Beer <dlbeer@gmail.com>
3 Oct 2016

This program is a utility which takes host and parasite trees (in NEXUS
format), and a link matrix (in CSV format), and generates an input file
for the Jane cophylogeny reconstruction software:

    https://www.cs.hmc.edu/~hadas/jane/

To run the GUI, open janex.exe. Use the options from the file menu to
import a host tree, parasite tree and H-P link matrix. Trees are read
from NEXUS files, where they must be the only tree in the file. Link
matrices are CSV tables, where the first row and first column contain
species labels, and the remaining cells contain either "1" or "true" to
indicate the presence of a link. By default, it's assumed that row
labels are host names and column labels are parasite names. You can swap
these by selecting "Transpose H-P link matrix" from the "Edit" menu.

The main area of the dialog will show a summary of the loaded data and
indicate any errors found (duplicate names, or non-existent species
referenced from the link matrix). Select "Export Jane tree file" from
the "File" menu to generate the output file.

There is also a command-line version (janex-cli.exe). Run this with
--help to get a list of options.

Bugs
----

Any bugs should be reported to me at the above email address. Note that
currently, time ranks are not supported (all species are given a rank of
1).