proseq is an integrated user-friendly windows based program for convenient sequence editing and evolutionary analysis. It is designed to simplify preparation and analysis of DNA sequence data sets in population genetic, phylogenetic and molecular ecology studies. Sequence editor features include editing of chromatogram files, contig assembly, sequence alignment, translation and other utilities. Analysis features include calculation of genetic diversity, divergence, population subdivision and gene flow with permutation-based significance testing and various tests of neutrality. A tool for coalescent simulations implements models with intragenic recombination, population subdivision and population growth.