Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm

(2023) Seong-Hwan Jun et al.   Algorithms for Molecular Biology

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

(2022) Cheng Ye et al.   BIOINFORMATICS

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

(2021) Yatish Turakhia et al.   NATURE GENETICS

Accuracy in Near-Perfect Virus Phylogenies

(2021) Joel O Wertheim et al.   SYSTEMATIC BIOLOGY

Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2

(2021) Dalang Yu et al.   BRIEFINGS IN BIOINFORMATICS

Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference

(2020) Chi Zhang et al.   SYSTEMATIC BIOLOGY

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

(2020) Shuhui Song et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

(2019) Sohta A Ishikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring whole-genome histories in large population datasets

(2019) Jerome Kelleher et al.   NATURE GENETICS

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Using Genotype Abundance to Improve Phylogenetic Inference

(2018) William S DeWitt et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

Quantifying MCMC Exploration of Phylogenetic Tree Space

(2015) Chris Whidden et al.   SYSTEMATIC BIOLOGY

Impacts of Terraces on Phylogenetic Inference

(2015) Michael J. Sanderson et al.   SYSTEMATIC BIOLOGY

Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny

(2011) Navodit Misra et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Quasi-median hulls in Hamming space are Steiner hulls

(2008) Hans-Jürgen Bandelt et al.   DISCRETE APPLIED MATHEMATICS