monophylizer
A web and command line tool to assess monophyly
Installation instructions
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.
Build status
Currently, the build status is:
How to cite
Marko, M., et al., 2016. Species-level para-and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera. Systematic Biology. 65(6):1024-1040 doi:10.1093/sysbio/syw044