|
Name |
|
Date |
Size |
#Lines |
LOC |
| .. | | 03-May-2022 | - |
| bin/ | H | 07-Dec-2019 | - | 8,289 | 4,318 |
| examples/ | H | 03-May-2022 | - | 7,045 | 4,395 |
| lib/ | H | 07-Dec-2019 | - | 223,832 | 84,845 |
| t/ | H | 07-Dec-2019 | - | 329,544 | 296,921 |
| AUTHORS | H A D | 07-Dec-2019 | 6.3 KiB | 247 | 124 |
| Changes | H A D | 07-Dec-2019 | 91 KiB | 2,188 | 1,767 |
| HACKING.md | H A D | 07-Dec-2019 | 7 KiB | 171 | 129 |
| LICENSE | H A D | 07-Dec-2019 | 17.9 KiB | 380 | 292 |
| MANIFEST | H A D | 07-Dec-2019 | 35.6 KiB | 1,395 | 1,394 |
| META.json | H A D | 07-Dec-2019 | 19.2 KiB | 594 | 592 |
| META.yml | H A D | 07-Dec-2019 | 11.9 KiB | 453 | 452 |
| Makefile.PL | H A D | 07-Dec-2019 | 5.9 KiB | 248 | 236 |
| README.md | H A D | 07-Dec-2019 | 2.6 KiB | 57 | 41 |
| dist.ini | H A D | 07-Dec-2019 | 1.8 KiB | 63 | 52 |
README.md
1[](http://dx.doi.org/10.5281/zenodo.16344)
2[](https://travis-ci.org/bioperl/bioperl-live)
3[](https://coveralls.io/r/bioperl/bioperl-live?branch=master)
4[](https://readthedocs.org/projects/bioperl/?badge=latest)
5
6# About BioPerl
7
8BioPerl is a project for development of free and open source Perl
9tools for computational molecular biology. For example, it includes
10classes for biological sequences, readers of multiple formats,
11sequence alignments, database searching objects, and interfaces to
12multiple programs such as EMBOSS, ClustalW, and BLAST.
13
14The BioPerl project has developed multiple module distributions for
15different purposes. The one named BioPerl (named after the project)
16provides the foundation for all others distributions.
17
18This is the repository for the BioPerl distribution only. Other
19distributions have [their own
20repositories](https://github.com/bioperl/).
21
22# Installation
23
24BioPerl distribution has the same name as the BioPerl. However, the
25BioPerl distribution only includes a subset of the project modules.
26Because of this, the meaning of "installing BioPerl" is rarely clear.
27Instead of "install BioPerl", the aim must be "install module X".
28
29[CPAN.org](https://www.cpan.org/modules/INSTALL.html) provides an
30overview on how to install and manage Perl modules but the bottom-line
31is:
32
331. find the module you need, for example `Bio::DB::EUtilities`
342. install it with `cpanm`, for example `cpanm Bio::DB::EUtilities`
35
36Alternatively, some Linux distributions have packaged BioPerl and have
37it available through their package manager.
38
39# Documentation and Support
40
41Documentation for individual modules is in POD and can also be read
42online at [metacpan](https://metacpan.org/pod/BioPerl). Useful
43documentation in the form of example code can also be found in the
44`examples/` and `bin/` directories.
45
46Additional resources and information about the project is available on
47the [project website](https://bioperl.org), with discussion happening
48on the [bioperl-l@bioperl.org](mailto:bioperl-l@bioperl.org) mailing
49list, and on the `#bioperl` channel of the freenode IRC server.
50
51Bug reports are handle on the distribution github page.
52
53# Development
54
55See the [`HACKING.md`](HACKING.md) file for details on the project
56structure, such as building from source and running the test suite.
57
){kind=link}
){kind=link}
){kind=link}