Software

 
DoFE - NOW INCLUDING NEUTRALITY INDEX ROUTINES
A program to calculate the distribution of fitness effects and rates of adaptive substitution from DNA sequence data using various methods developed by us and others. Methods implemented include Fay, Wycoff and Wu (2001), Smith and Eyre-walker (2002), Bierne and Eyre-Walker (2004), Eyre-Walker, Woolfit and Phelps (2006), Eyre-Walker and Keightley (2009) and Stoletzki and Eyre-Walker (2011). Click on icon to download versions for DoFE 3.0 - Mac.zip, DoFE 3.0 - windows.zip and DoFE_3.0_linux.zip along with documentation.Software_files/DoFE%203.0%20-%20Mac.zipSoftware_files/DoFE%203.0%20-%20Mac.zipSoftware_files/DoFE%203.0%20-%20windows.zipSoftware_files/DoFE_3.0_linux.zipSoftware_files/DoFE%203.0%20-%20Mac_1.zipshapeimage_1_link_0shapeimage_1_link_1shapeimage_1_link_2shapeimage_1_link_3
Piganeau and Eyre-Walker (2003) PNAS
A mathematica notebook to run the method for estimating the distribution of fitness effects given in Piganeau and Eyre-Walker (2003) PNAS.Software_files/Piganeau%20%26%20EW%20method_1.nb
RecombiTest
A web-based suite of programs to test for recombination using Maynard Smith’s MaxChi test, Sawyer’s geneconv test and two methods that look at the correlation between linkage disequilibrium and the distance between sites. For further details see Piganeau, Gardner and Eyre-Walker (2004) A broad survey of recombination in animal mitochondria. Mol. Biol. Evol. 21, 2319-2325.http://www.lifesci.sussex.ac.uk/CSE/test/index.php
Genetic architecture
The equations from Eyre-Walker (2010) The genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. PNAS 107, 1752Software_files/PNAS%20equations.nb