Bio::Phylo - Phyloinformatic analysis using Perl
Perl Other
Latest commit 2fd9be3 Jun 19, 2016 @rvosa adding Yandell's unit test


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.