BioJava is an open-source project dedicated to providing Java tools for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures.
The goal of the biojava project is to facilitate rapid application development for bioinformatics. It is a package that contains class files and objects that implement Java code to be used for a variety of things.
BioJava is used in many different projects. These include Dazzle (a BioJava based DAS server), Bioclipse (an open source workbench for chemo- and bioinformatics with powerful editing and visualization capabilities), Bioweka (an open source biological data mining application), and Geneious (a molecular biology toolkit).
Key Features
- Objects for manipulating biological sequences.
- File parsers.
- DAS client and server support.
- Access to BioSQL and Ensembl databases.
- Tools for making sequence analysis GUIs.
- Powerful analysis and statistical routines including a dynamic programming toolkit.
Website: biojava.org
Support: Cookbook, GitHub Code Repository
Developer: Thomas Down, Michael Heuer, David Huen, Matthew Pocock, Mark Schreiber and many others
License: GNU Lesser General Public License v2.1
BioJava is written in Java. Learn Java 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 |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| 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 |
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