BioPerl
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| - | = | + | = Information = |
* Web site: http://www.bioperl.org/ | * Web site: http://www.bioperl.org/ | ||
| - | * Described version: | + | * Described version: 1.6.1 |
* Licensing: Dual - Perl Artistic License or GNU General Public License v3 | * Licensing: Dual - Perl Artistic License or GNU General Public License v3 | ||
| - | * User documentation: | + | * User documentation: http://www.bioperl.org/wiki/Category:Documentation |
| - | * Download: | + | * Download: http://www.bioperl.org/wiki/Getting_BioPerl#BioPerl_Releases |
| - | * Source code: | + | * Source code: http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz |
== Authors/Maintainers == | == Authors/Maintainers == | ||
| - | + | Bioperl developers: [mailto:bioperl-l@bioperl.org bioperl-l@bioperl.org] | |
== Summary == | == Summary == | ||
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== Usage Overview == | == Usage Overview == | ||
| - | * | + | * Installation on [http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix Unix] and on [http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Windows] |
| + | * [http://www.bioperl.org/wiki/HOWTOs#BioPerl_HOWTOs HowTo] | ||
| + | * [http://www.bioperl.org/wiki/Bptutorial.pl Tutorial] and tutorial [http://www.bioperl.org/wiki/Tutorials documents] | ||
== Dependacies == | == Dependacies == | ||
| - | * | + | * Unix |
| + | ** Perl 5.6.1 or later; version 5.8 or greater is recommended. | ||
| + | ** make. For Mac OS X, this requires installing the [http://developer.apple.com/tools/macosxtools.html Xcode Developer Tools]. | ||
| + | * Windows | ||
| + | ** [http://www.activestate.com/activeperl?mp=1 ActivePerl] >= 5.8.8.819 | ||
| + | |||
| + | [http://www.bioperl.org/wiki/BioPerl_Dependencies other] dependencies | ||
== HP-SEE Applications == | == HP-SEE Applications == | ||
| - | * | + | * DeepAligner (Deep sequencing for short fragment alignment) [http://wiki.hp-see.eu/index.php/DeepAligner] |
| + | * DiseaseGene (In-silico Disease Gene Mapper) [http://wiki.hp-see.eu/index.php/DiseaseGene] | ||
== Resource Centers == | == Resource Centers == | ||
| Line 48: | Line 57: | ||
== Usage by other projects and communities == | == Usage by other projects and communities == | ||
* If any | * If any | ||
| + | |||
| + | == Recommendations for Configuration and Usage == | ||
| + | |||
| + | Need to be installed to user space. | ||
Latest revision as of 23:15, 24 April 2012
Contents |
Information
- Web site: http://www.bioperl.org/
- Described version: 1.6.1
- Licensing: Dual - Perl Artistic License or GNU General Public License v3
- User documentation: http://www.bioperl.org/wiki/Category:Documentation
- Download: http://www.bioperl.org/wiki/Getting_BioPerl#BioPerl_Releases
- Source code: http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
Authors/Maintainers
Bioperl developers: bioperl-l@bioperl.org
Summary
BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the BioPerl-live repository consist of the core of the functionality of BioPerl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules. Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, BioPerl enables one to develop scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
Features
- Listed features
Architectural/Functional Overview
- high level design info, how it works, performance - may be a link, or several links
Usage Overview
Dependacies
- Unix
- Perl 5.6.1 or later; version 5.8 or greater is recommended.
- make. For Mac OS X, this requires installing the Xcode Developer Tools.
- Windows
- ActivePerl >= 5.8.8.819
other dependencies
HP-SEE Applications
- DeepAligner (Deep sequencing for short fragment alignment) [1]
- DiseaseGene (In-silico Disease Gene Mapper) [2]
Resource Centers
- RCs supporting it (with version number if not the same as above)
Usage by other projects and communities
- If any
Recommendations for Configuration and Usage
Need to be installed to user space.
