Biopython specifications

Information


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
Wikipedia https://en.wikipedia.org/wiki/Biopython

Subtool


  • Bio.Phylo

Download


Versioning


Add your version

Documentation


Maintainers


Biopython articles

Biopython citations

 (2)
2015
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 (http://biopython.org/, 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 […]

2014
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

star_border star_border star_border star_border star_border
star star star star star

Zulko

star_border star_border star_border star_border star_border
star star star star star
Desktop
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).