PyCogent: A toolkit for making sense from sequence

Rob Knight; Peter Maxwell; Amanda Birmingham; Jason Carnes; J. Gregory Caporaso; Brett C. Easton; Michael Eaton; Micah Hamady; Helen Lindsay; Zongzhi Liu; Catherine Lozupone; Daniel McDonald; Michael Robeson; Raymond Sammut; Sandra Smit; Matthew J. Wakefield; Jeremy Widmann; Shandy Wikman; Stephanie Wilson; Hua Ying; Gavin A. Huttley

doi:10.1186/gb-2007-8-8-r171

PyCogent: A toolkit for making sense from sequence

Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J. Gregory Caporaso, Brett C. Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J. Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua YingGavin A. Huttley

Electrical Engineering and Computer Science

Research output: Contribution to journal › Article

134 Scopus citations

Abstract

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 http://sourceforge.net/projects/pycogent.

Original language	English (US)
Article number	R171
Journal	Genome Biology
Volume	8
Issue number	8
DOIs	https://doi.org/10.1186/gb-2007-8-8-r171
State	Published - Aug 21 2007

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ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Cite this

Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M., Hamady, M., Lindsay, H., Liu, Z., Lozupone, C., McDonald, D., Robeson, M., Sammut, R., Smit, S., Wakefield, M. J., Widmann, J., Wikman, S., Wilson, S., ... Huttley, G. A. (2007). PyCogent: A toolkit for making sense from sequence. Genome Biology, 8(8), [R171]. https://doi.org/10.1186/gb-2007-8-8-r171

PyCogent : A toolkit for making sense from sequence. / Knight, Rob; Maxwell, Peter; Birmingham, Amanda; Carnes, Jason; Caporaso, J. Gregory; Easton, Brett C.; Eaton, Michael; Hamady, Micah; Lindsay, Helen; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Robeson, Michael; Sammut, Raymond; Smit, Sandra; Wakefield, Matthew J.; Widmann, Jeremy; Wikman, Shandy; Wilson, Stephanie; Ying, Hua; Huttley, Gavin A.

In: Genome Biology, Vol. 8, No. 8, R171, 21.08.2007.

Research output: Contribution to journal › Article

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 2007, 'PyCogent: A toolkit for making sense from sequence', Genome Biology, vol. 8, no. 8, R171. https://doi.org/10.1186/gb-2007-8-8-r171

Knight, Rob ; Maxwell, Peter ; Birmingham, Amanda ; Carnes, Jason ; Caporaso, J. Gregory ; Easton, Brett C. ; Eaton, Michael ; Hamady, Micah ; Lindsay, Helen ; Liu, Zongzhi ; Lozupone, Catherine ; McDonald, Daniel ; Robeson, Michael ; Sammut, Raymond ; Smit, Sandra ; Wakefield, Matthew J. ; Widmann, Jeremy ; Wikman, Shandy ; Wilson, Stephanie ; Ying, Hua ; Huttley, Gavin A. / PyCogent : A toolkit for making sense from sequence. In: Genome Biology. 2007 ; Vol. 8, No. 8.

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Access to Document

10.1186/gb-2007-8-8-r171