New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics.

ABSTRACT: Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate goal of generating a phylogeny. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results. Many tools are also difficult to install and may lack adequate user resources. Here, we describe a program that uses freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance compared to other commonly used bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, and on one large set each of

SUBMITTER: Knyshov A 

PROVIDER: S-EPMC8019319 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature