Wrapper for BEAGLE library
C Perl Shell
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lib/Bio/Phylo
t
.gitignore
MANIFEST
Makefile.PL
README
beagle.i
beagle.pm
beagle_wrap.c
build.sh

README

Bio::Phylo::Beagle - wrapper around the Beagle library

This is perl wrapper code that allows one to use Bio::Phylo's data handling
capabilities to interface with the Beagle library for likelihood calculations:

* Beagle     - http://dx.doi.org/10.1093/sysbio/syr100
* Bio::Phylo - http://dx.doi.org/10.1186/1471-2105-12-63

It is based on the SWIG bindings that were orginally developed for python by
Simon Frost:

http://code.google.com/p/beagle-lib/source/browse/trunk/examples/swig_python/README

I developed this on a MacBook Pro with OS X snow leopard. I used the svn
revision 1082 of Beagle to build against. I found that I needed to update
my SWIG to version 2.0.4, with pcre (both from source).

On operating systems that support pkg-config and backticks you should be
able to build and install this library. To ensure that everything is OK
you should first check to see that pkg-config returns the right values.
Try this:

pkg-config --cflags hmsbeagle-1

This should return something like the following (exact path may differ
depending on your BEAGLE installation):

-I/usr/local/include/libhmsbeagle-1

If that is indeed the case, you should be able to build this library 
using the following commands:

perl Makefile.PL
make
make test
(sudo make install) <-- don't do this while these wrappers are experimental

The unit test script t/test_simple.t does the same computation as the python
test.py script in the Beagle-lib source tree, demonstrating most of the
current functionality.