BioJulia is a bioinformatics and computational biology infrastructure project, built with and for the julia language for technical computing.
Bio is the flagship package of the project.
Bio is actually better described as a meta-package. It actually
consolidates many other smaller packages in the BioJulia package ecosystem
and makes them easier to install and use together, with less worry about
version compatiblity and dependencies.
Bio has the current feature modules:
Bio.Seq: A biological sequences module (provided by BioSequences.jl)
- Biological symbols (DNA, RNA and amino acid)
- Biological sequences
- Sequence search algorithms
- Readers for FASTA, FASTQ and .2bit file formats
Bio.Align: Sequence alignment (provided by BioAlignments.jl)
- Alignment data structures
- Pairwise alignment algorithms
- Reader for SAM and BAM file formats
Bio.Intervals: Genomic intervals and annotations (provided by GenomicFeatures.jl)
- Genomic intervals with annotations
- Readers for BED, bigWig, bigBed and GFF3 file formats
Bio.Structure: Molecular structures (provided by BioStructures.jl)
- Macromolecular structures (e.g. proteins)
- Reader for PDB file format
Bio.Var: Biological variation (provided by GeneticVariation.jl)
- Mutation counting
- Genetic and evolutionary distances
- Readers for VCF and BCF file formats
Bio.Phylo: Phylogenetics (provided by Phylogenies.jl)
- Phylogenetic trees
Bio.Services: APIs to other services (provided by BioServices.jl)
- Entrez utilities (E-utilities)
Bio.Tools: A module for running command line tools (provided by BioTools.jl)
- Run BLAST and parse its output
Install Bio from the Julia REPL:
using Pkg add("Bio") # Pkg.add("Bio") for julia prior to v0.7
If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.
Bio is tested against Julia
0.6 and current
0.7-dev on Linux, OS X, and
|Latest release||Latest build status|
We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.
Take a look at the CONTRIBUTING file provided with every BioJulia package package for detailed contributor and maintainer guidelines.
We also welcome financial contributions in full transparency on our open collective. Anyone can file an expense. If the expense makes sense for the development of the community, it will be "merged" in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.
Backers & Sponsors
Thank you to all our backers and sponsors!
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