Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.

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

SUBMITTER: Dylus D 

PROVIDER: S-EPMC10791578 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature