Divide and conquer sequential Monte Carlo for phylogenetics
Sean Jewell · cIRcle (University of British Columbia) · 2015
Recently reconstructing evolutionary histories has become a computational issue due to the increased availability of genetic sequencing data and relaxations of classical modelling assumptions. This thesis specializes a Divide & conquer sequential Monte Carlo (DCSMC) inference algorithm to phylogenetics to address these challenges. In phylogenetics, the tree structure used to represent evolutionary histories provides a model decomposition used for DCSMC. In particular, speciation events are used to recursively decompose the model into subproblems. Each subproblem is approximated by an independent population of weighted particles, which are merged and propagated to create an ancestral population. This approach provides the flexibility to relax classical assumptions on large trees by parallelizing these recursions.