Margarita infers genealogies from population genotype data and uses these to map disease loci.

These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events.

[Genome Research Limited]



There are two stages to the analysis. First, we infer plausible ARGs using a heuristic algorithm, which can handle unphased and missing data. Second, we test the genealogical tree at each locus for a clustering of the disease cases beneath a branch. Since the true ARG is unknown, we average this analysis over an ensemble of inferred ARGs.


High resolution figures from the paper:

The method is described in:

  • Mapping trait loci by use of inferred ancestral recombination graphs.

    Minichiello MJ and Durbin R

    American journal of human genetics 2006;79;5;910-22


Margarita requires Java. See the documentation for further details.

FTP downloads

Example input and output files

  • Example 1 - A case-control study with phased sequences.
  • Example 2 - The same case-control study as Example 1, but with unphased sequences.
  • Output from running Margarita on Example 1.



Questions about Margarita can be directed to Richard Durbin.

* quick link -