Computational methods I developed

MIMAR* - MCMC estimation of the Isolation-Migration model Allowing for Recombination

MIMAR is a Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. It uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and in contrast to previous methods, allows for intralocus recombination. Note that you need to know the ancestral allele at each polymorphic site in order to calculate the summary statistics (although I now provide an untested program which allows to use data for which no ancestral sequence is available). The method is described in Becquet and Przewroski (2007) Genome Research.
Last Update: December 17 2010. Please refer to this page for any information on future versions.
The tar file includes the following:
  • The program MIMAR
  • The program MIMARgof. This program allows one to perform a goodness of fit test on the posterior distributions estimated by MIMAR.
  • The program MIMARsim. This program simulates data sets under the isolation-migration model and generates an input file analyzable by MIMAR.
  • All the associated help files. I tried to provide all the relevant information in the file MIMARdoc.pdf. However, if you find some parts unclear, have more questions, or discover a bug in any of these programs, do not hesitate to contact me.
  • The programs MIMAR_noanc, MIMARgof_noanc and MIMARsim_noanc which assume unknown ancestral states.

  • * In Spanish and Portuguese, mimar is a transitive verb which means:

  • (acariciar) to caress, to cuddle, to fondle, to pet
  • (consentir) to pamper, to spoil, to indulge, to coddle, to cosset, to cosher, to spoon-feed, to mollycoddle
  • (tratar con cariño) to fuss, to fuss over