Viral phylogenies have wide use: studying evolution, tracing the origin of epidemics, establishing dominant mode of transmission, identifying the apparition of drug resistance, even tracking individual body compartments.
Many tools infer ancestral state, few interpret it. Hence the need for a fast, easy to use exploratory tool, PhyloType. Given a phylogeny, it allows inference of ancestral traits, along with hypothesis testing, with a speed which makes it applicable for exploratory analysis and/or datasets with thousands of samples.
Define: Viral Phylotype. a subset of studied taxa that share a common history. "History" has a twofold definition. First, based on the phylogeny: a phylotype must be part of a clade, and the root of the clade must be the MRCA of the members of the phylotype. Second, common traits or annotations: if the phylotype root has a unique annotation A (which is conserved), then all members of the phylotype also have annotation A.
The term phylotype is common in microbiology, and refers to a (taxon-neutral) classification based on phylogenetic relationship to other organisms.
Method: Infer ancestral annotations using maximum parsimony. Use this annotation to induce a set of phylotypes, defined by MRCA and path-conservation. Apply combinatorial, numerical, and statistical criteria to select relevant phylotypes.
One example is the study of the origin of the Albanian HIV epidemic.