Biopython specifications


Unique identifier OMICS_04850
Name Biopython
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.71
Stability Stable
Requirements matplotlib, Graphviz, NetworkX
Maintained Yes


  • Bio.Phylo



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Biopython articles

Biopython citations

PMCID: 4530583

[…] the alignments that overlap the mouse peak and include hg19 were extracted. we calculated the human mouse pairwise alignment for each multiple alignment using the “globalms” function of biopython (, version 1.59; python version 2.71). the highest scoring pairwise alignment formed base of the orthologous region in human. this region was extended on either side […]

PMCID: 4094930

[…] reads across the collection, reads were mapped to the accessory genome component using bwa v0.7.3 [66]. the coverage plots were then generated using samtools [67]. heatmaps were generated using biopython [68]., wph has consulted for glaxosmithkline. kpk has consulted for pfizer, glaxosmithkline and merck. kgk has an investigator-initiated study sponsored by glaxosmithkline. sdb […]

Biopython institution(s)
Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain; James Hutton Institute, Invergowrie, UK; Harvard School of Public Health Bioinformatics Core, Boston, MA, USA
Biopython funding source(s)
Supported by Google Summer of Code 2009, the National Evolutionary Synthesis Center (NESCent) Phyloinformatics program and a FI-DGR from AGAUR.

Biopython review

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Probably the most complete and generic library for Bioinformatics in Python, BioPython enjoys a broad user base, years of features contributions, and an extensive documentation.

We use Biopython mainly for standard formats (Genbank/Fasta/AB1) import/export, and for basic restriction/ligation simulations. For more advanced uses we generally need to build a functionality on top of Biopython, or use an existing library that does that.

One downside of Biopython is the presence of many sub-packages from different subdomains of bioinformatics, which makes the library very big and hard to navigate (also hard to fully maintain I imagine).