DEPP: Deep Learning Enables Extending Species Trees using Single Genes.

ABSTRACT: Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real da

SUBMITTER: Jiang Y 

PROVIDER: S-EPMC10198656 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature