Minus the Error: Estimating / and Testing for Natural Selection in the Presence of Residual Alignment Errors.

Errors in multiple sequence alignments (MSAs) are known to bias many comparative evolutionary methods. In the context of natural selection analyses, specifically codon evolutionary models, excessive rates of false positives result. A characteristic signature of error-driven findings is unrealistically high estimates of dN/dS (e.

Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019-2020 Epidemic in the United States.

For the first time, we describe phylogenomic signatures of an epidemic lineage of vesicular stomatitis Indiana virus (VSIV). We applied multiple evolutionary analyses to a dataset of 87 full-length genome sequences representing the circulation of an epidemic VSIV lineage in the US between 2019 and 2020. Based on phylogenetic analyses, we predicted the ancestral relationship of this lineage with a specific group of isolates circulating in the endemic zone of Chiapas, Mexico.

Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion.

Highly pathogenic avian influenza H5N1 clade 2.3.4.

Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants.

Background: Detecting very minor (< 1%) subpopulations using next-generation sequencing is a critical need for multiple applications, including the detection of drug resistant pathogens and somatic variant detection in oncology. A recently available sequencing approach termed 'sequencing by binding (SBB)' claims to have higher base calling accuracy data "out of the box." This paper evaluates the utility of using SBB for the detection of ultra-rare drug resistant subpopulations in Mycobacterium tuberculosis (Mtb) using a targeted amplicon assay and compares the performance of SBB to single molecule overlapping reads (SMOR) error corrected sequencing by synthesis (SBS) data.

The effect of information integration on team communication in a simulated submarine control room task.

Submarine control rooms are characterised by dedicated individual roles for information types (e.g. Sonar operator processes sound energy), with individuals verbally reporting the information that they receive to other team members to help resolve uncertainty in the operational environment (low information integration).