Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …

Background Due to recent advances in whole genome shotgun sequencing and assembly
technologies, the financial cost of decoding an organism's DNA has been drastically …

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …

A fundamental question in microbiology is whether there is continuum of genetic diversity
among genomes, or clear species boundaries prevail instead. Whole-genome similarity …

High-throughput short-read metagenomics has enabled large-scale species-level analysis
and functional characterization of microbial communities. Microbiomes often contain multiple …

The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in
large-scale microbial analysis. Though mapping approaches can be used to find differences …

Background Multiple genome alignment remains a challenging problem. Effects of
recombination including rearrangement, segmental duplication, gain, and loss can create a …

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic
species assignments can be inconsistent with whole genome information for a significant …

There is increasing interest in employing shotgun sequencing, rather than amplicon
sequencing, to analyze microbiome samples. Typical projects may involve hundreds of …

Motivation: The relative ease and low cost of current generation sequencing technologies
has led to a dramatic increase in the number of sequenced genomes for species across the …