Bio::Phylo - Phyloinformatic analysis using Perl
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experimental starting to adapt to Bio::Phylo API Apr 2, 2015
script removing svn cruft Apr 2, 2011
t adding Yandell's unit test Jun 19, 2016
.travis.yml adding travis YAML Mar 27, 2014
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MANIFEST.skip added skip pattern for travis yml Mar 27, 2014
Makefile.PL EU::MM apparently now wants Package::Name instead of Package-Name Mar 27, 2014 Update Apr 13, 2015
inheritance Adding Bio::Phylo code Apr 2, 2011 Adding Bio::Phylo code Apr 2, 2011
podinherit Adding Bio::Phylo code Apr 2, 2011


An object-oriented toolkit for analyzing and manipulating phyloinformatic data.


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.


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 for the latest release number visit:

Currently, the build status at Travis is:

Build Status


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. For example, when you get an error message at runtime that alerts you to a missing dependency. If any of such additional CPAN modules are found to be missing at installation time, a warning will be emitted, but installation and unit testing can continue.

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

  • perl Makefile.PL
  • make
  • make test (Optional, runs unit tests, which should pass)
  • 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)


  • Rutger Vos
  • Jason Caravas
  • Klaas Hartmann
  • Mark A. Jensen
  • Chase Miller
  • Aki Mimoto
  • Hannes Hettling
  • Florent Angly


Please report any bugs or feature requests on the GitHub bug tracker:


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 (; and Arne Mooers from the FAB* lab ( 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 no. 237046.


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


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 2005-2015 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.