EPIK: precise and scalable evolutionary placement with informative k-mers.

ABSTRACT:

Motivation

Phylogenetic placement enables phylogenetic analysis of massive collections of newly sequenced DNA, when de novo tree inference is too unreliable or inefficient. Assuming that a high-quality reference tree is available, the idea is to seek the correct placement of the new sequences in that tree. Recently, alignment-free approaches to phylogenetic placement have emerged, both to circumvent the need to align the new sequences and to avoid the calculations that typically follow the alignment step. A promising approach is based on the inference of k-mers that can be potentially related to the reference sequences, also called phylo-k-mers. However, its usage is limited by the time and memory-consuming stage of reference data preprocessing and the large numbers of k-mers to co

SUBMITTER: Romashchenko N 

PROVIDER: S-EPMC10701097 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature