Bio-Phylo - README

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)

AUTHOR

Rutger Vos, rutgeraldo@gmail.com, http://rutgervos.blogspot.com

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 author 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); Jason Caravas, Klaas Hartmann, Mark A. Jensen, Chase Miller and Aki Mimoto for their contributions (code and otherwise) to this project; and Arne Mooers from the FAB* lab (http://www.sfu.ca/~fabstar) for comments and requests.

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