C programs

Below are some C programs we have written for various purposes. Most are just plain text files but apparently Harvard's OpenScholar does not support a ".c" file type, so they are zipped; ones with multiple files are tarred and gzipped. Feel free to use these programs for whatever purposes you want and to modify them to suit your needs. We have checked them very thoroughly for bugs, but there may still be some. We would appreciate hearing about any you do find. Of course, we can't guarantee these will work for you and we especially can't be held responsible if any of these fail after adaptation to other purposes. Still, we would be happy to assist in getting these programs to work for you. If you use any of these in preparing a publication, please cite the appropriate paper.

  • - coalescence within a population pedigree as in Wakeley et al (2012) Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent.
  • - exact numerical calculation of the joint site-frequency spectrum as in Wakeley and Hey (1997) Estimating ancestral population parameters.
  • - described in Wakeley and Aliacar (2001) Gene genealogies in a metapopulation.
  • - described in Wakeley and Takahashi (2003) Gene genealogies when the sample exceeds the effective size of the population.
  • SharMot.02sep04.tgz - described in Castillo-Davis, Hartl and Achaz (2004) Cis-regulatory and protein evolution in orthologous and duplicate genes.
  • RepSeek - described in Achaz, Boyer, Rocha, Viari and Coissac (2006) Extracting approximate repeats from large DNA sequences.