Jane tree file generator ======================== Version 0.4 Daniel Beer <firstname.lastname@example.org> 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).