{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Dylus D"],"funding":["Swiss National Science Foundation","NIAID NIH HHS","NHGRI NIH HHS"],"pubmed_abstract":["The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolu"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2022.04.18.488678"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9774205"],"repository":["biostudies-literature"],"pubmed_title":["Read2Tree: scalable and accurate phylogenetic trees from raw reads."],"pmcid":["PMC9774205"],"funding_grant_id":["183723","186397","U19 AI144297","UM1 HG008898"],"pubmed_authors":["Sedlazeck FJ","Majidian S","Dylus D","Dessimoz C","Altenhoff A"],"additional_accession":[]},"is_claimable":false,"name":"Read2Tree: scalable and accurate phylogenetic trees from raw reads.","description":"The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolu","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Dec","modification":"2026-06-20T03:25:27.636Z","creation":"2025-04-06T08:52:15.44Z"},"accession":"S-EPMC9774205","cross_references":{"pubmed":["36561179"],"doi":["10.1101/2022.04.18.488678"]}}