phyBWT2: phylogeny reconstruction via eBWT positional clustering

Indexing Highly Repetitive String Collections, Part II

(2021) Gonzalo Navarro   ACM COMPUTING SURVEYS

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction

(2021) Andreas Rempel et al.   BIOINFORMATICS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees

(2020) Martin R Smith   BIOINFORMATICS

gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections

(2020) Felipe A. Louza et al.   Algorithms for Molecular Biology

Metagenomic analysis through the extended Burrows-Wheeler transform

(2020) Veronica Guerrini et al.   BMC BIOINFORMATICS

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

(2020) Nicola Prezza et al.   BMC BIOINFORMATICS

Space-efficient construction of compressed suffix trees

(2020) Nicola Prezza et al.   THEORETICAL COMPUTER SCIENCE

External memory BWT and LCP computation for sequence collections with applications

(2019) Lavinia Egidi et al.   Algorithms for Molecular Biology

SNPs detection by eBWT positional clustering

(2019) Nicola Prezza et al.   Algorithms for Molecular Biology

Prefix-free parsing for building big BWTs

(2019) Christina Boucher et al.   Algorithms for Molecular Biology

Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes

(2019) Lorenzo Tattini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interspecific hybridization facilitates niche adaptation in beer yeast

(2019) Brigida Gallone et al.   Nature Ecology & Evolution

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

(2016) Michelle Kendall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Editorial: Alignment-free methods in computational biology

(2014) S. Vinga   BRIEFINGS IN BIOINFORMATICS

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Colored range queries and document retrieval

(2012) Travis Gagie et al.   THEORETICAL COMPUTER SCIENCE

Lightweight algorithms for constructing and inverting the BWT of string collections

(2012) Markus J. Bauer et al.   THEORETICAL COMPUTER SCIENCE

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella

(2011) Elizabeth Skippington et al.   BMC GENOMICS

The evolution of HIV: Inferences using phylogenetics

(2011) Eduardo Castro-Nallar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Burrows–Wheeler similarity distribution between biological sequences based on Burrows–Wheeler transform

(2009) Lianping Yang et al.   JOURNAL OF THEORETICAL BIOLOGY