[nexml]
phylogenetic data in xmlThe 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.
Directory listing
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:
- SVG.pm
- XML::LibXML
- IO::String
- Math::Random
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.
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/perl/ \
perl
Name Last modified Size Description
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
lib/ 17-Dec-2008 14:31 - Folder
script/ 04-Mar-2010 10:40 - Folder
t/ 04-Mar-2010 12:45 - Folder