Yatish Turakhia

The paper introduces viral_usher, a tool for scalable viral phylogenetics, and demonstrates that replication machinery explains most variance in viral mutation spectra.

ROADIES-XP enables efficient incremental species tree updates from raw genomic assemblies using GPU acceleration, achieving high speedups and maintaining topological accuracy.

DIPPER is a GPU-accelerated distance-based phylogenetic tool that achieves ultrafast and ultralarge phylogenetic reconstruction with improved speed, accuracy, and memory efficiency.

Panmap efficiently aligns, genotypes, and places reads on large pangenomes using phylogenetic compression, enabling rapid analysis of up to 8 million genomes.

This paper introduces PanMAN, a compressed pangenome data structure that captures evolutionary and mutational histories, achieving significant compression and enabling more efficient pangenomic analysis.

The paper introduces larch, a tool that explores the space of optimal phylogenetic trees to find more parsimonious trees and increase diversity in the set of optimal solutions.

The paper identifies highly recurrent multi-nucleotide mutations in SARS-CoV-2 and shows they are linked to transcription regulatory sequences, affecting computational evolutionary biology analyses.

ROADIES infers species trees from raw genome assemblies quickly and accurately, outperforming existing methods in speed while maintaining comparable quality.

This study compares pangoLEARN and pUShER for SARS-CoV-2 lineage assignment, finding pUShER more stable and accurate across pangolin versions.

RIVET identifies and tracks potential SARS-CoV-2 recombinants using advanced algorithms and provides a web interface for accelerated analysis.

The paper introduces MAPLE, a new phylogenetic analysis method that scales to large datasets by improving computational efficiency, outperforming existing tools like FastTree and RAxML-NG.

The paper introduces phastSim, a tool for efficiently simulating sequence evolution on large phylogenetic trees, particularly for SARS-CoV-2-like datasets.

The paper develops a phylogenetic package to handle pandemic-scale SARS-CoV-2 genomic data, enabling real-time analysis and visualization of large mutation-annotated phylogenetic trees.

This study compares online and de novo phylogenetic methods for SARS-CoV-2, finding that maximum parsimony online approaches are more accurate and efficient than maximum likelihood or de novo methods.

The paper introduces a daily-updated database of SARS-CoV-2 mutation-annotated trees and associated tools for querying and manipulating the data.

The paper introduces UShER, a method for ultrafast phylogenetic placement of SARS-CoV-2 sequences, enabling real-time genomic contact tracing and maintaining an updated reference phylogeny.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

The paper identifies 500+ high-confidence gene loss events in 58 mammals using automated methods, revealing some linked to human disease and early lethality.

Darwin accelerates genomic sequence alignment with hardware acceleration, achieving significant speed and energy efficiency improvements over existing methods.