PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data.

ABSTRACT:

Premise

The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming.

Methods and results

PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference

SUBMITTER: Cai L 

PROVIDER: S-EPMC9215275 | biostudies-literature | 2022 May-Jun

REPOSITORIES: biostudies-literature