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.
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:
Bio.Seq: Biological sequences- Biological symbols (DNA, RNA and amino acid)
- Biological sequences
- Sequence search algorithms
- Readers for FASTA, FASTQ and .2bit file formats
Bio.Align: Sequence alignment- Alignment data structures
- Pairwise alignment algorithms
Bio.Intervals: Genomic intervals and annotations- Genomic intervals with annotations
- Readers for BED and BigBed file formats
Bio.Structure: Molecular structures- Macromolecular structures (e.g. proteins)
- Reader for PDB file format
Bio.Var: Biological variation- Mutation counting
- Genetic and evolutionary distances
Bio.Phylo: Phylogenetics- Phylogenetic trees
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Documentation
Read the reference manual here: http://biojulia.github.io/Bio.jl/latest.
Install
Bio.jl is a registered package in the official package management system and can be installed with a command:
julia> Pkg.add("Bio")
If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.
Contributing
We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features. If you have a question about contributing, our Gitter chat room would be the best place to communicate with other users and developers.
Roadmap
Our roadmap is on the wiki: https://github.com/BioJulia/Bio.jl/wiki/roadmap.