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Seminar 15/11: Simon Whelan

posted Nov 16, 2017, 5:16 AM by Allison Hsiang
Our next SPG seminar will be given by Simon Whelan, researcher at the Department of Ecology and Genetics at Uppsala University. Simon will be speaking about sequence alignment and its impact on phylogenetic inference. 

Title: The problem of sequence alignment in phylogenetics
Date: November 15, 2017
Time: 15:00-16:00
Place: KÖL Lunch Room (Frescativägen 54)

Abstract: Inferring evolutionary histories and processes from sets of homologous sequences is a joint problem of sequence alignment and phylogenetic inference. Computational convenience led to the widespread adoption of the two-step process, whereby those problems are separated and solved in succession. Nearly all research in molecular evolution has focussed on the final phylogenetic inference problem, where models of substitution and tree shape have the potential to provide insights into natural selection and population structures. All of this progress rests upon the assumption that the sequence alignment step is correct. 

This talk discusses the gap between the perceived and real accuracy of the solutions to the sequence alignment problem and their impact on phylogenetics. I will explore first some of the evidence that errors in sequence alignment are real and have a demonstrable effect on downstream phylogenetic analyses, introducing systematic biases and affecting the biological conclusions drawn from these studies. Next I will discuss approaches that take existing alignments and try to identify and remove errors in them. These include existing alignment filtering approaches and some new approaches to processing alignments currently under development in my research group. Finally I will present an alternative to the two-step approach that can directly estimate evolutionary parameters, including the phylogenetic tree and selection, directly from sequences without assuming a fixed alignment.