This software provides a collection of Perl modules that can be used to build bioinformatics solutions. It is open source and offers a range of tools for processing data in Perl.
BioPerl is a software package that is built in an object-oriented manner, with many modules depending on each other to achieve various tasks. Within the bioperl-live repository, there is a collection of modules which are essentially the core of the BioPerl functionality.
In addition to this core, users can also access auxiliary modules such as bioperl-gui, which deals with graphical interfaces, bioperl-db for persistent storage in RDBMS, bioperl-pipeline, which helps to automate bioinformatic analyses, and the Run package, used for running and parsing results from hundreds of bioinformatics applications. All of these additional packages are available as Subversion modules in the BioPerl repository, designed to make life easy for end-users.
BioPerl toolkit is divided into several different packages. While there are a variety of packages available, the Core package is the most commonly used package, providing necessary parsers to process various data. This package is the basic requirement for all other BioPerl packages. Other packages include Run package, BioPerl db package, and Network package. Run package provides wrappers for executing a total of sixty common bioinformatics applications, BioPerl db package is designed to store sequence and annotation data in a BioSQL relational database, and the Network package analyzes and processes protein-protein interaction data.
For those interested in installing BioPerl, it is advised to use the Fink installation method. To install the developer release of BioPerl, users can just issue the "fink install bioperl-pmXXX" command, where XXX refers to the Perl version that is installed on your system (e.g. 586 or 588).
Lastly, it is important to note that BioPerl is licensed under the same terms as Perl itself, which is dually-licensed under the terms of the GNU GPL or the Perl Artistic License. All in all, BioPerl is an effective, well-rounded software suite that is designed to make bioinformatics analyses easier, streamlined, and more intuitive.
In addition to this core, users can also access auxiliary modules such as bioperl-gui, which deals with graphical interfaces, bioperl-db for persistent storage in RDBMS, bioperl-pipeline, which helps to automate bioinformatic analyses, and the Run package, used for running and parsing results from hundreds of bioinformatics applications. All of these additional packages are available as Subversion modules in the BioPerl repository, designed to make life easy for end-users.
BioPerl toolkit is divided into several different packages. While there are a variety of packages available, the Core package is the most commonly used package, providing necessary parsers to process various data. This package is the basic requirement for all other BioPerl packages. Other packages include Run package, BioPerl db package, and Network package. Run package provides wrappers for executing a total of sixty common bioinformatics applications, BioPerl db package is designed to store sequence and annotation data in a BioSQL relational database, and the Network package analyzes and processes protein-protein interaction data.
For those interested in installing BioPerl, it is advised to use the Fink installation method. To install the developer release of BioPerl, users can just issue the "fink install bioperl-pmXXX" command, where XXX refers to the Perl version that is installed on your system (e.g. 586 or 588).
Lastly, it is important to note that BioPerl is licensed under the same terms as Perl itself, which is dually-licensed under the terms of the GNU GPL or the Perl Artistic License. All in all, BioPerl is an effective, well-rounded software suite that is designed to make bioinformatics analyses easier, streamlined, and more intuitive.
What's New
Version 1.6.0: N/A