Solving the master equation for Indels

BMC Bioinformatics
Ian Holmes

Abstract

Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances.

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Citations

Sep 22, 2018·Systematic Biology·Eli Levy KarinTal Pupko
May 22, 2019·Systematic Biology·Alberto Pascual-GarcíaUgo Bastolla
Aug 14, 2020·Genome Biology and Evolution·Kelsey Aadland, Bryan Kolaczkowski
Feb 8, 2019·BMC Bioinformatics·Farzad FarnoudJehoshua Bruck
Feb 9, 2020·Genome Biology·David LähnemannAlexander Schönhuth

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Software Mentioned

Seq
DAWG
XRate
indel
INDELible
PAML
PHYLIP
- PUZZLE
Gen
RevBayes

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