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Author

Yatish Turakhia

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Open access Sep 2026

Real-time accessible phylogenetics for every highly sampled virus

The scale of viral genome sequencing has outpaced the phylogenetic tools traditionally used to analyze it, as highlighted by the COVID-19 pandemic. We present viral_usher, a unified framework for scalable viral phylogenetics built on UShER. viral_usher is a containerized command-line tool that constructs mutation-annot...

Angie S. Hinrichs, Lily Karim, Yatish Turakhia et al. · 0 citations
Open access Aug 2026

ROADIES-XP: GPU Acceleration and Phylogenetic Update Improve Scalability of Species Tree Inference from Raw Genomic Assemblies

Most large-scale whole-genome sequencing projects release assemblies incrementally in phases. However, existing phylogenomic workflows typically assume a static set of genomic sequences, thus requiring a full de novo species tree reconstruction whenever new genomes need to be incorporated into the analysis, which is bo...

Anshu Gupta, Wen-Chieh Lo, Siavash Mirarab et al. · 0 citations
Open access Jul 2026

metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis

Metagenomic sequencing pipeline metaWEPP is presented, a novel computational pipeline that achieves near-haplotype resolution in metagenomic analysis for species with adequate representation in reference genome biobanks and having sufficient sequencing depth and genome coverage.

Pranav Gangwar, Qi-Wen Xu, Jaden Seangmany et al. · 0 citations

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