  Somatic variants can be used as lineage markers for the phylogenetic
reconstruction of cancer evolution. Since somatic phylogenetics is complicated
by sample heterogeneity, novel specialized tree-building methods are required
for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for
Cancer Heterogeneity and Evolution), a novel method that automates the
phylogenetic inference of cancer progression from multiple somatic samples.
LICHeE uses variant allele frequencies of SSNVs obtained by deep sequencing to
reconstruct multi-sample cell lineage trees and infer the subclonal composition
of the samples. LICHeE is open-sourced and available at
http://viq854.github.io/lichee.
