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Open Access Highly Accessed Research article

Analysis of epistatic interactions and fitness landscapes using a new geometric approach

Niko Beerenwinkel1*, Lior Pachter2, Bernd Sturmfels2, Santiago F Elena3 and Richard E Lenski4*

Author Affiliations

1 Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA

2 Department of Mathematics, University of California, Berkeley, CA 94720, USA

3 Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain

4 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA

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BMC Evolutionary Biology 2007, 7:60  doi:10.1186/1471-2148-7-60

Published: 13 April 2007

Additional files

Additional file 1:

Instructions for calculating the Markov basis and triangulation of a dataset with Macaulay 2.

Format: PDF Size: 96KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 2:

Macaulay 2 file for computing Markov bases of interaction spaces and triangulations of genotopes. (This program requires Macaulay 2 version 0.0.95 to be installed. See additional file 1 for instructions.)

Format: M2 Size: 4KB Download file

Open Data

Additional file 3:

Examples of fitness landscape files to be processed with the program fitness.m2 (additional file 2).

Format: ZIP Size: 2KB Download file

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Additional file 4:

Minimal Markov basis of the interaction space.

Format: TXT Size: 3KB Download file

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Additional file 5:

Geometry of the fitness landscape.

Format: TXT Size: 39KB Download file

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