BioPerl is a collection of Perl tools for computational molecular biology.
The BioPerl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g. Ensembl.
BioPerl 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 used by many large and small academic laboratories, and pharmaceutical companies of all sizes.
Key Features
- Accessing nucleotide and peptide sequence data from local and remote databases.
- Transforming formats of database/ file records.
- Manipulating individual sequences.
- Searching for similar sequences.
- Creating and manipulating sequence alignments.
- Searching for genes and other structures on genomic DNA.
- Developing machine readable sequence annotations.
- Provides the base for many different bioinformatic tools including: SynBrowse, TFBS, MIMOX, BioParser, GeneComber, and many others.
Website: bioperl.org
Support: GitHub Code Repository
Developer: Sendu Bala, Chris Dagdigian, Christopher Fields, Mark Jensen, Hilmar Lapp, Heikki Lehväslaiho, Aaron Mackey, Brian Osborne, Jason Stajic, Lincoln Stein, and many others
License: GNU General Public License and Perl Artistic License
BioPerl is written in Perl. Learn Perl with our recommended free books and free tutorials.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| samtools | Manipulate next-generation sequencing data |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
| Taverna Workbench | For designing and executing bioinformatics workflows |
| geWorkbench | Software platform for integrated genomic data analysis |
| Bioclipse | Rich-client platform chemistry and biology workbench |
Read our verdict in the software roundup.
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