• Dawg: the best simulator of neutral evolution in DNA sequences. Version 2 is in development, and it will harder, better, faster, stronger, and easier to use.
  • Ngila: pairwise sequences alignment with robust evolutionary models.
  • SPAGeDi: spatial analysis of genetic data. Developed by Olivier Hardy and Xavier Vekemans.  I have ported their code to Unix-like systems.
  • Red Lynx: A flexible population genetic simulator that runs in your browser. Great for teaching.
  • PICS-Ord: A method to extract phylogeny information from hard-to-align regions of multiple sequence alignments.
  • SoFoS: Site Frequency Spectrum Rescaler: A little javascript applet that can rescale site frequency spectra to a common sample size
  • Klineage: A forward simulator of ancestral lineages. Checkout from the subversion repository