ArticleNature biotechnology2024
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Beyond formic acid: Peptides in carpenter ant venoms aid in disease protection.Science advances · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.The Journal of heredity · 2026Article
- OrthoGarden: a pipeline for propagating phylogenetic trees for nonmodel organisms from short reads and de novo genome assemblies.Molecular biology and evolution · 2026Article
- An Equatorial Hemispheric Barrier Shapes the Diversification of Migratory Belenois Butterflies.Molecular ecology · 2026Article
- Phylogenomics unravels the early divergence and diversification in Bignoniaceae.Plant diversity · 2026Article
- Ongoing structural changes highlight the dynamic nature of chloroplast genomes.Nucleic acids research · 2026Article
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.Molecular ecology resources · 2026Article
- GeneMiner2: Accurate and Automated Recovery of Genes From Genome Skimming Data.Molecular ecology resources · 2026Article
- Exploring the genetic landscape of sesame: whole genome sequencing reveals distinct Egyptian lineages and SNP variability.Molecular genetics and genomics : MGG · 2026Article
- Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-LeavedGenes · 2026Article
- Detection and characterization of neonatal cytomegalovirus through nanopore sequencing using flongle flow cells: Pilot study in Philadelphia, Pennsylvania.Journal of virological methods · 2026Article
- Reassessing the Evolutionary Relationships ofBiology · 2025Article
- Morphological and Genetic Heterogeneity inEcology and evolution · 2025Article
- Unraveling phylogenetic conflicts and adaptive evolution in Chiroptera using large-scale mitogenomes and nuclear genes.Science China. Life sciences · 2025Article
- Genomic Data Suggests Pathways of Modern White Poplar (Plants (Basel, Switzerland) · 2025Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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5 authors.
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Abstract
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
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