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Open Access Publications from the University of California

PyCogent: A toolkit for making sense from sequence

  • Author(s): Knight, R
  • Maxwell, P
  • Birmingham, A
  • Carnes, J
  • Caporaso, JG
  • Easton, BC
  • Eaton, M
  • Hamady, M
  • Lindsay, H
  • Liu, Z
  • Lozupone, C
  • McDonald, D
  • Robeson, M
  • Sammut, R
  • Smit, S
  • Wakefield, MJ
  • Widmann, J
  • Wikman, S
  • Wilson, S
  • Ying, H
  • Huttley, GA
  • et al.

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 © 2007 Knight et al.; licensee BioMed Central Ltd.

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