TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

ABSTRACT:

Motivation

Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites but millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate and fas

SUBMITTER: Caraballo-Ortiz MA 

PROVIDER: S-EPMC9113349 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature