MCALIGN: alignment of noncoding DNA sequences based on explicit models of indel evolution.
MLGENOMEU: Estimation of mutation parameters from mutation accumulation experiments.
DFE-alpha: 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: 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].