Analysis of epistatic interactions and fitness landscapes using a new geometric approach
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
BMC Evolutionary Biology 2007, 7:60 doi:10.1186/1471-2148-7-60Published: 13 April 2007
Additional file 1:
Instructions for calculating the Markov basis and triangulation of a dataset with Macaulay 2.
Format: PDF Size: 96KB Download file
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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
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
Additional file 4:
Minimal Markov basis of the interaction space.
Format: TXT Size: 3KB Download file
Additional file 5:
Geometry of the fitness landscape.
Format: TXT Size: 39KB Download file