Frequentist Estimation of Evolutionary History of Sequences with Substitutions & Indels

The evolutionary history of molecules is described by a tree structure called phylogeny, which is inferred from genomic sequences. Phylogenies are used for testing biological hypotheses with applications ranging from medicine to ecology. Inferring ancestral molecular states on phylogenetic trees can help us in testing such hypotheses. Phylogenetic inferences typically rely on character substitution models that describe only point mutations, but ignore insertions and deletions. The goal of this project is to develop a new maximum likelihood method for ancestral sequences reconstruction that accommodates insertions and deletions, and therefore is more biologically meaningful.