PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.

ABSTRACT: Next-generation sequencing of pathogen quasispecies within a host yields data sets of tens to hundreds of unique sequences. However, the full data set often contains thousands of sequences, because many of those unique sequences have multiple identical copies. Data sets of this size represent a computational challenge for currently available Bayesian phylogenetic and phylodynamic methods. Through simulations, we explore how large data sets with duplicate sequences affect the speed and accuracy of phylogenetic and phylodynamic analysis within BEAST 2. We show that using unique sequences only leads to biases, and using a random subset of sequences yields imprecise parameter estimates. To overcome these shortcomings, we introduce PIQMEE, a BEAST 2 add-on that produces reliable parameter estim

SUBMITTER: Boskova V 

PROVIDER: S-EPMC7530608 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature