README.md
1
2
3Bio::Phylo
4==========
5
6An object-oriented toolkit for analyzing and manipulating phyloinformatic data.
7
8DESCRIPTION
9-----------
10Phylogenetics is the branch of evolutionary biology that deals with reconstructing and
11analyzing the tree of life. This distribution provides objects and methods to aid in
12handling and analyzing phylogenetic data.
13
14COMPATIBILITY
15-------------
16Bio::Phylo installs without problems on most popular, current platforms (Win32, OSX,
17Linux, Solaris, IRIX, FreeBSD, OpenBSD, NetBSD), on Perl versions >= 5.8.0
18
19For a list of automated test results for the latest release number visit:
20
21http://testers.cpan.org/show/Bio-Phylo.html
22
23Currently, the build status at Travis for the head revision is:
24
25[](https://travis-ci.org/rvosa/bio-phylo)
26
27INSTALLATION
28------------
29Bio::Phylo has no dependencies for its core install. However, some additional
30functionality will not work (e.g. XML parsing) until the CPAN module that enables
31it has been installed (e.g. XML::Twig). You can install these at a later date if
32and when need arises. For example, when you get an error message at runtime that
33alerts you to a missing dependency. If any of such additional CPAN modules are
34found to be missing at installation time, a warning will be emitted, but
35installation and unit testing can continue.
36
37To install the Bio::Phylo distribution itself, run the following commands:
38
39 perl Makefile.PL
40 make
41 make test # Optional, runs unit tests, which should pass
42 make install
43
44(For platform specific information on what 'make' command to use, check "perl -V:make".
45On Windows this usually returns "make='nmake';", which means you'll need the free 'nmake'
46utility)
47
48CONTRIBUTORS
49------------
50The following people have contributed code to the project:
51* Rutger Vos
52* Hannes Hettling
53* Florent Angly
54* Jason Caravas
55* Klaas Hartmann
56* Mark A. Jensen
57* Moritz Lenz
58* Chase Miller
59* Aki Mimoto
60* Jan Willem Wijnands
61
62The following people have provided feedback through issues and reviews:
63* Denis Baurain
64* Chris Fields
65* Shlomi Fish
66* Jean-Marc Frigerio
67* Andreas J. König
68* Hilmar Lapp
69* Nicolas Lenfant
70* Sébastien Moretti
71* Slaven Rezić
72* `Seiler`
73* `scorpio17`
74
75BUGS
76----
77Please report any bugs or feature requests on the GitHub bug tracker:
78
79https://github.com/rvosa/bio-phylo/issues
80
81ACKNOWLEDGEMENTS
82----------------
83The authors would like to thank the BioPerl project for providing the community
84with a terrific toolkit that other software, such as this, can be built on
85(http://www.bioperl.org); and Arne Mooers from the FAB* lab (http://www.sfu.ca/~fabstar)
86for comments and requests.
87
88The research leading to these results has received funding from the European
89Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement
90no. 237046.
91
92SEE ALSO
93--------
94**Documentation** This distribution contains a high-level overview that can be
95accessed using the perldoc documentation system. The documentation is at
96[Bio::Phylo::Manual](lib/Bio/Phylo/Manual.pod) and can be viewed (after
97installation) on the command line:
98
99 perldoc Bio::Phylo::Manual
100
101**Optional extensions** Compatible with this distribution are two optional
102packages that can be installed alongside Bio::Phylo. These packages are:
103- [Bio::PhyloXS](http://search.cpan.org/dist/Bio-PhyloXS/) - which provides
104 faster implementations (in C) of the core objects of Bio::Phylo. The source
105 code repository is [here](https://github.com/rvosa/bio-phylo-xs), and the
106 v0.1.0 release is tagged as
107 [10.5281/zenodo.1010362](http://doi.org/10.5281/zenodo.1010362).
108- [Bio::Phylo::Forest::DBTree](http://search.cpan.org/dist/Bio-Phylo-Forest-DBTree/) -
109 which provides an object-relational mapping of the core objects of Bio::Phylo.
110 The source code repository is
111 [here](https://github.com/rvosa/bio-phylo-forest-dbtree), and the v0.1.2
112 release is tagged as
113 [10.5281/zenodo.1035856](http://doi.org/10.5281/zenodo.1035856).
114
115CITATION
116--------
117If you use Bio::Phylo in published research, please cite it:
118
119**Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen
120and Chase Miller**, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
121_BMC Bioinformatics_ 12:63.
122doi:[10.1186/1471-2105-12-63](http://doi.org/10.1186/1471-2105-12-63)
123
124COPYRIGHT & LICENSE
125-------------------
126Copyright 2005-2017 Rutger Vos, All Rights Reserved. This program is free software;
127you can redistribute it and/or modify it under the same terms as Perl itself, i.e.
128a choice between the following licenses:
129- [The Artistic License](COPYING)
130- [GNU General Public License v3.0](LICENSE)
131
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