PyCogent: a toolkit for making sense from sequence

Genome Biol. 2007;8(8):R171. doi: 10.1186/gb-2007-8-8-r171.


We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • BRCA1 Protein / genetics
  • Databases, Genetic
  • Genomics / methods*
  • Humans
  • Phylogeny
  • Protein Conformation
  • Proteobacteria / classification
  • Proteobacteria / genetics
  • Sequence Analysis / methods*
  • Software*
  • von Willebrand Factor / chemistry
  • von Willebrand Factor / genetics


  • BRCA1 Protein
  • von Willebrand Factor