Bio::Phylo::Forest::DBTree

An object-oriented API to operate on very large phylogenies stored in portable databases

Release

The most recent release is:

Requires

• Bio::Phylo
• DBIx::Class
• DBD::SQLite
• An installation of sqlite3

Installation

This package can be installed in the standard ways, e.g. after downloading from this repository, using the ExtUtils::MakeMaker workflow:

$ perl Makefile.PL
$ make
$ sudo make install

Alternatively, the cpanm workflow can be used to install directly from github, i.e.

$ sudo cpanm git://github.com/rvosa/bio-phylo-forest-dbtree.git

Or, opting for the most recent release from CPAN, using:

$ sudo cpanm Bio::Phylo::Forest::DBTree

BUGS

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

https://github.com/rvosa/bio-phylo-forest-dbtree/issues

BUILD STATUS

Currently, the build status of the head revision at Travis is:

The test results of the CPAN releases are here:

http://www.cpantesters.org/distro/B/Bio-Phylo-Forest-DBTree.html

COPYRIGHT & LICENSE

Copyright 2013-2017 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:

• The Artistic License
• GNU General Public License v3.0

SEE ALSO

Several curated, large phylogenies released by ongoing projects are made available as database files that this distribution can operate on. These are:

• PhyloTree (van Oven et al., 2009) - 10.6084/m9.figshare.4620757.v1
• D-Place (Kirby et al., 2016) - 10.6084/m9.figshare.4620217.v1
• NCBI taxonomy (Federhen, 2011) - 10.6084/m9.figshare.4620733.v1
• Green Genes (DeSantis et al., 2006) - 10.6084/m9.figshare.4620214.v1