IM
documentation

updated 10/23/2007
IM is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. Large numbers of loci can be studied simultaneously, and different mutation models can be used. IM estimates the divergence time and the migrations having occurred in the ancestry of two populations, which might have grown exponentially since split. Important limitations of the basic model are that it cannot account for changes in population sizes, and it cannot account for the sizes of founding populations
IMa also allows log likelihood ratio tests of nested demographic models. IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for

• written in C
• unix/linux
• dos/windows
• Mac

contains the data for all loci to be considered

• line 1 - arbitrary text, usually explaining the content of the file
  • After line 1, but before line 2, comments can be included to provide explanatory information. Each line of comment must begin with a ‘#’
• line 2 - two population names, for populations 1 and 2 respectively, separated by one or more spaces
• line 3 - the number of loci in the data set (integer)
• line 4 - basic information for locus 1. This line contains at least five items separated by one or more spaces
  1. Locus name (no spaces within the name)
  2. n1, the sample size for population 1
  3. n2, the sample size for population 2
  4. the length of the sequence
  5. ……