Bio.jl Documentation

This documentation site contains The Bio.jl User Manual

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
  • Reader for SAM and BAM file formats

  • Bio.Intervals: Genomic intervals and annotations

  • Genomic intervals with annotations

  • Readers for BED, BigBed and GFF3 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
  • Readers for VCF and BCF file formats

  • Bio.Phylo: Phylogenetics

  • Phylogenetic trees

  • Bio.Services: APIs to other services

  • Entrez utilities (E-utilities)