Bio::Phylo::Forest::DBTree
==========================
An object-oriented API to operate on very large phylogenies stored in portable databases
Release
-------
The most recent release is:
[](https://zenodo.org/badge/latestdoi/8080160)
Requires
--------
* [Bio::Phylo](http://search.cpan.org/dist/Bio-Phylo/)
* [DBIx::Class](http://search.cpan.org/dist/DBIx-Class/)
* [DBD::SQLite](http://search.cpan.org/dist/DBD-SQLite/)
* An installation of [sqlite3](https://www.sqlite.org/)
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](http://search.cpan.org/dist/Bio-Phylo-Forest-DBTree/)
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:
[](https://travis-ci.org/rvosa/bio-phylo-forest-dbtree)
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](COPYING)
- [GNU General Public License v3.0](LICENSE)
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][1]) - [10.6084/m9.figshare.4620757.v1](http://doi.org/10.6084/m9.figshare.4620757.v1)
- D-Place ([Kirby et al., 2016][2]) - [10.6084/m9.figshare.4620217.v1](http://doi.org/10.6084/m9.figshare.4620217.v1)
- NCBI taxonomy ([Federhen, 2011][3]) - [10.6084/m9.figshare.4620733.v1](http://doi.org/10.6084/m9.figshare.4620733.v1)
- Green Genes ([DeSantis et al., 2006][4]) - [10.6084/m9.figshare.4620214.v1](http://doi.org/10.6084/m9.figshare.4620214.v1)
[1]: http://doi.org/10.1002/humu.20921
[2]: http://doi.org/10.1371/journal.pone.0158391
[3]: http://doi.org/10.1093/nar/gkr1178
[4]: http://doi.org/10.1128/AEM.03006-05