Foliage is a software library for efficiently constructing ancestral recombination graphs in memory. It aims to facilitate the implementation of various algorithms and statistical analysis by providing a coherent API for the graphs. It is also capable cropping the graphs along the genome coordinates, drawing Graphviz diagrams of the graphs and correlation heat maps that measure linkage across the genome by comparing the distance between the marginal trees. The integrated margarita library, written by Mark Minichiello, can be used to infer plausible ARGs from fastPHASE haplotype sequences.
Foliage is released under the terms of the GNU GPL and was written during my work period at the Richard Durbin lab at the Sanger Institute between November 2006 to February 2008.
An '''Ancestral Recombination Graph''' is a directed acyclic graph composed of the trees that relate individuals in a population at each position in the genome. The trees vary as one moves along the chromosome, because of ancestral recombination events.
The Apache Solr OpenBitSet is used as the underlying binary vector representation class.
