Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Genome wide orthology inference and dNdS estimation

Program for estimating dN/dS in overlapping genes (OLGs)

Fast heuristic methods of detecting adaptive evolution in protein-coding genes.

CRBHits - a reimplementation of the Conditional Reciprocal Best Hit algorithm in R.

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Evolutionary genomics of chromosomal inversions in Atlantic herring

EDEN: evolutionary dynamics within environments

It is a powerful tool for aligning nucleotide sequences based on protein alignments, translating nucleotide sequences to protein, and generating phylogenetic trees using Biopython.

the user interface for EDEN - Evolutionary Dynamics within Environments