Phyloinformatic analysis using Perl
Perl
Switch branches/tags
Clone or download
Pull request Compare This branch is 433 commits behind rvosa:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
experimental
lib/Bio
script
t
.gitignore
COPYING
LICENSE
MANIFEST.skip
Makefile.PL
README.txt
inheritance
inheritance.sh
podinherit

README.txt

Bio::Phylo - An object-oriented Perl toolkit for analyzing and manipulating phyloinformatic data. 

DESCRIPTION

Phylogenetics is the branch of evolutionary biology that deals with reconstructing and analyzing the tree of life. This distribution provides objects and methods to aid in handling and analyzing phylogenetic data.

COMPATABILITY
 
Bio::Phylo installs without problems on most popular, current platforms (Win32, OSX, Linux, Solaris, IRIX, FreeBSD, OpenBSD, NetBSD), on Perl versions >= 5.8.0

For a list of automated test results visit:

http://testers.cpan.org/show/Bio-Phylo.html

INSTALLATION

Bio::Phylo has no dependencies for its core install. However, some additional functionality will not work (e.g. XML parsing) until the CPAN module that enables it has been installed (e.g. XML::Twig). You can install these at a later date if and when need arises. If any of such additional CPAN modules are found to be missing at installation time, a warning will be emitted, but installation can continue.

To install the Bio::Phylo distribution itself, run the
following commands: 

perl Makefile.PL
make
make test
make install
 
(For platform specific information on what 'make' command to use, check "perl -V:make". On Windows this usually returns "make='nmake';", which means you'll need the free 'nmake' utility)

AUTHORS

Rutger Vos
Jason Caravas
Klaas Hartmann
Mark A. Jensen
Chase Miller
Aki Mimoto

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web 
interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo I will be notified, 
and then you'll automatically be notified of progress on your bug as I make changes. 
 
ACKNOWLEDGEMENTS

The authors would like to thank the BioPerl project for providing the community
with a terrific toolkit that other software, such as this, can be built on
(http://www.bioperl.org); and Arne Mooers from the FAB* lab (http://www.sfu.ca/~fabstar) for
comments and requests.

The research leading to these results has received funding from the [European
Community's] Seventh Framework Programme ([FP7/2007-2013] under grant agreement
n� [237046].

SEE ALSO

Read the manual: perldoc Bio::Phylo::Manual

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen
and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
BMC Bioinformatics 12:63.
doi:10.1186/1471-2105-12-63

COPYRIGHT & LICENSE

Copyright 2005-2011 Rutger Vos, All Rights Reserved. This program is free software; 
you can redistribute it and/or modify it under the same terms as Perl itself.