To Join via Zoom: To join this seminar virtually, please request Zoom connection details from headsec [at] stat.ubc.ca
Abstract: Phylogenetic tree reconstruction and multiple sequence alignment are fundamental tasks in phylogenetics that should ideally be performed jointly, since trees and alignments are inherently circularly dependent. In reality, however, the two structures are more often than not inferred sequentially as independent estimates. Moreover, aligners infer MSAs that contain gaps representing insertions and deletions, while most standard likelihood-based phylogenetic tree reconstruction tools take the MSA as input and proceed to filter out gappy columns due to the lack means to include them in the phylogenetic likelihood computation. A way to solve this disparity in modelling is to include evolutionary models that explicitly account for indels in the likelihood, allowing us to use all available data in inference without having to hack our way around unequal sequence lengths.
In this talk, we will discuss the status quo in phylogenetic modelling and talk about the current work in Maria Anisimova's group on an efficient joint inference method that will hopefully bring us one step closer to making our expectations a reality.