A web and command line tool to assess monophyly
This tool depends on the Bio::Phylo toolkit, which needs to be installed from the comprehensive perl archive network here: http://search.cpan.org/dist/Bio-Phylo
Installation from CPAN is a standard system administration task for which ample documentation is available on the internet, and which is easy for UNIX-capable system administrators and ICT support staffers. Consult them if you don't know how to do this.
To run the tool on the command line, do this:
perl monophylizer.pl -infile newickFile.nwk > outputTable.tsv
Additional command line arguments (which you almost certainly won't need) are documented in the source code of monophylizer.pl
To run this tool as a web service, the following steps are necessary:
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Place monophylizer.pl in a location where it will be executed as a perl CGI script by your web server. This will probably involve copying it into a folder called cgi-bin (linux/unix) or CGI-Executables (OSX). In addition, it may need to be set to "executable" and the first line of the script may need to be changed to point to the correct location of the perl interpreter if it is not located at /usr/bin/perl
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Place monophylizer.html and sorttable.js in a location for plain text (not executable) files.
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If the javascript file sorttable.js is not in the "document root", you will need to edit monophylizer.pl such that the output HTML can find it. This is at time of writing at line 250.
Currently, the build status is:
Pending publication of the method, this tool can be cited as:
Vos, R.A., 2015. Monophylizer: A web and command line tool to assess monophyly. [doi: 10.5281/zenodo.16874]
