nexml - index of /nexml/perl/

Skip to: Site menu | Main content

The future data exchange standard is here!

nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Process nexml data

Directory listing

~ / nexml / perl
digg reddit del.icio.us facebook | Wed Mar 10 01:48:54 2010 —

This subdirectory contains a release candidate for Bio::Phylo with nexml parser support.

To build this, you may want to get several optional prerequisites from CPAN first:

And for the nexml extension you must install XML::Twig first.

The code in this subdirectory is released under the standard perl licensing scheme, which is a dual system supplying users a choice between the artistic license and the GNU public license.

Provided you have the prerequisites, you can build this code by issuing:
$ perl Makefile.PL
$ make
Which places the built code in a 'blib' subdirectory of this folder.

To run the test suite (which might fail at this stage of the development), issue:
$ make test
For NeXML tests, set environment variable NEXML_ROOT to the checked out trunk/nexml folder of the nexml project. For BioPerl tests, set environment variable BIOPERL_LIVE_ROOT to the checked trunk/bioperl-live folder.

To install (but don't do that just yet, instead point your $PERL5LIB to the lib/ folder), issue:
$ make install

For examples of validation and translation, check out the full source tree from the sourceforge project and peruse nexml/validator.cgi and nexml/nex2xml.cgi, respectively.

To download the contents of this folder using svn:
svn co \
    https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/perl/ \
    perl 
Icon  Name                 Last modified      Size  Description
[DIR] Parent Directory                          -   Folder
[   ] BioPhylo.kpf         03-Mar-2010 15:45  1.8K  Folder
[   ] COPYING              04-Mar-2009 16:06  5.8K  Software license
[   ] LICENSE              04-Mar-2009 16:06   34K  Software license
[   ] MANIFEST.skip        04-Mar-2010 12:35  457   Exclude patterns
[   ] Makefile.PL          17-Dec-2008 14:31  914   Make file
[   ] README.html          16-Jun-2009 07:00  1.5K  HTML document
[   ] README.txt           02-Mar-2010 09:15  2.1K  Plain text file
[   ] build.sh             22-Feb-2009 16:16  432   Unix shell script
[DIR] lib/                 17-Dec-2008 14:31    -   Folder
[DIR] script/              04-Mar-2010 10:40    -   Folder
[DIR] t/                   04-Mar-2010 12:45    -   Folder