As the flagship package of the BioJulia organisation, Bio.jl provides core modules containing efficient data types and algorithms, that most bioinformaticians and biologists would want to use for analyses or for building their own applications.
Bio.jl is built on top of the Julia programming language, a high-level and high-performance programming language for technical computing. Bio.jl and Julia are open source and their source codes are immediately available to the public.
Modules and Functionality
Bio.jl provides programmable components for quick prototyping of new analyses and algorithms. These components are carefully tuned to achieve the best performance without sacrificing the usability of the dynamic programming language. The following modules are currently part of the package and actively developed as submodules:
- Biological symbols (DNA, RNA, and amino acids)
- Biological sequences
- Sequence search algorithms
- Readers for FASTA, FASTQ and .2bit file formats
- Biological sequence alignment
- Alignment data structures
- Pairwise alignment algorithms
- Intervals and annotations
- Genomic intervals with annotations
- Readers for BED and BigBed file formats
- Molecular structures
- Macromolecular structures (e.g. proteins)
- Reader for the PDB file format
- Biological variation
- Mutation counting
- Genetic and evolutionary distances
- Phylogenetic trees
In a Julia console, enter:
Julia’s package manager will try to find the latest released version and install it.
Alternatively, to install the bleeding edge of a branch use:
Then use the Bio submodules in a script like so:
Created and maintained by the BioJulia team
If you would like to contribute to any BioJulia module, please refer to the contributing guidelines.