Biopython: freely available Python tools for computational molecular biology and bioinformatics
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Summary
Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
- Type
- article
- Published
- 2009-03-20
- Cited by
- 5,706
- References
- 27
- Access
- Open access
- OpenAlex
- https://openalex.org/W19304878
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:28555614
Keywords
Fantasy, Humanities, Art, Literature
References
- Bacterial comparative genomics
- EMBOSS: the European Molecular Biology Open Software Suite.
- Improved tools for biological sequence comparison.
- xBASE, a collection of online databases for bacterial comparative genomics
- genepop’007: a complete re‐implementation of the genepop software for Windows and Linux
- Biopython: Python tools for computational biology
- NEXUS: an extensible file format for systematic information.
- BioJava: an open-source framework for bioinformatics
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
- Python for Scientific Computing
- Evaluating loci for use in the genetic analysis of population structure
- WASABI: an automated sequence processing system for multigene phylogenies.
- Open source clustering software.
- The Bioperl toolkit: Perl modules for the life sciences.
- The molecular modeling toolkit: A new approach to molecular simulations
- EMBL Nucleotide Sequence Database in 2006
- The Universal Protein Resource (UniProt)
- PDB file parser and structure class implemented in Python
- SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
- The Pfam protein families database
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- Reference datasets of tufA and UPA markers to identify algae in metabarcoding surveys
- PON-SC – program for identifying steric clashes caused by amino acid substitutions
- Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses
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