Spectrum is a program for jointly inferring population structure and recombination events using multi-locus SNP haplotypes. Assuming a number of founder chromosomes, it infers the association of each individual with founders and generates an ancestral spectrum, which displays genetic population structure and reveals details of the genetic diversity of each individual with respect to recovered founder chromosomes. It also estimates empirical recombination rates and hotspots jointly with the population structure.

Example: Analysis of HapMap data

  • Inferred population structure of HapMap four population. Different colors correspond to different founder chromosomes, and each individual is represented by a thin vertical line partitioned into colored segment whose length is proportional to the fraction of chromosome associated with each founder.

  • Estimated recombination rates along chromosomal positions

  • Frequencies of each founder along chromosome positions