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Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.

Caporaso JG, Smit S, Easton BC, Hunter L, Huttley GA, Knight R.

BMC Evol Biol. 2008 Dec 3;8:327. doi: 10.1186/1471-2148-8-327.


PyCogent: a toolkit for making sense from sequence.

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.

Genome Biol. 2007;8(8):R171.

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