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 the following required dependencies: Scalar::Util (core) Test::More (core) IO::File (core) IO::String (non-core, but installs everywhere) And the following optional dependencies: SVG (to draw trees as SVG vector drawings) Math::Random (to simulate trees) XML::Twig (to parse nexml) These modules are all available from http://www.cpan.org, and should install without problems on most platforms. To install the Bio::Phylo distribution, 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 Win32 this usually returns "make='nmake';", which means you'll need the 'nmake' utility: http://support.microsoft.com/default.aspx?scid=kb;en-us;Q132084) AUTHOR Rutger Vos, rutgeraldo@gmail.com, http://rutgervos.blogspot.com BUGS Please report any bugs or feature requests to bug-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=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 COPYRIGHT & LICENSE Copyright 2005-2010 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.