Joint Alignment and Tree Inference

Multiple sequence alignment and phylogenetic tree inference are connected problems that are often solved as independent steps in the inference process. Several attempts at doing simultaneous inference have been made, however currently the available methods are greatly limited by their computational complexity and can only handle small datasets. In this manuscript we introduce a combinatorial optimisation approach that will allow us to resolve the circularity of the problem and efficiently infer both alignments and trees under maximum likelihood.