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:
http://testers.cpan.org/show/Bio-Phylo.html
Currently, the build status at Travis for the head revision is:
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)
The following people have contributed code to the project:
- Rutger Vos
- Hannes Hettling
- Florent Angly
- Jason Caravas
- Klaas Hartmann
- Mark A. Jensen
- Moritz Lenz
- Chase Miller
- Aki Mimoto
- Jan Willem Wijnands
The following people have provided feedback through issues and reviews:
- Denis Baurain
- Chris Fields
- Shlomi Fish
- Jean-Marc Frigerio
- Andreas J. König
- Hilmar Lapp
- Nicolas Lenfant
- Sébastien Moretti
- Slaven Rezić
Seilerscorpio17
Please report any bugs or feature requests on the GitHub bug tracker:
https://github.com/rvosa/bio-phylo/issues
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 no. 237046.
Documentation This distribution contains a high-level overview that can be accessed using the perldoc documentation system. The documentation is at Bio::Phylo::Manual and can be viewed (after installation) on the command line:
perldoc Bio::Phylo::Manual
Optional extensions Compatible with this distribution are two optional packages that can be installed alongside Bio::Phylo. These packages are:
- Bio::PhyloXS - which provides faster implementations (in C) of the core objects of Bio::Phylo. The source code repository is here, and the v0.1.0 release is tagged as 10.5281/zenodo.1010362.
- Bio::Phylo::Forest::DBTree - which provides an object-relational mapping of the core objects of Bio::Phylo. The source code repository is here, and the v0.1.2 release is tagged as 10.5281/zenodo.1035856.
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 2005-2017 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, i.e. a choice between the following licenses: