Software resources


MCALIGN: alignment of noncoding DNA sequences based on explicit models of indel evolution.



MLGENOMEU: Estimation of mutation parameters from mutation accumulation experiments.



DFE-alpha/DFE-adaptive:


Download source code with build instructions and data files here. Alternatively, DFE-alpha/DFE-adaptive can be run by uploading your data to the following servers:


DFE-alpha server. Inference of the distribution of fitness effects of new deleterious mutations and the fraction (
α) and relative rate (ωa) of adaptive substitutions based on folded nucleotide polymorphism site frequency spectra and between-species nucleotide divergence by the method of Keightley and Eyre-Walker (2007) [PDF] and Eyre-Walker and Keightley (2009) [PDF].


DFE-adaptive server: Inference of the distribution of fitness effects of new mutations, including the fraction (
pa) and fitness effects (sa) of adaptive mutations, based on unfolded nucleotide polymorphism site frequency spectra by the method of Schneider et al. (2011) [PDF].