ArticleApplications in plant sciences
PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data.
Article in Applications in plant sciences. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens.Molecular ecology resources · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae.Plant diversity · 2026Article
- A composite universal DNA signature for the tree of life.Nature ecology & evolution · 2025Article
- A curated benchmark dataset for molecular identification based on genome skimming.Scientific data · 2025Article
- Article
- Subfamily evolution analysis using nuclear and chloroplast data from the same reads.Scientific reports · 2025Article
- A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.Molecular ecology resources · 2025Article
- Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.Genome research · 2023Article
- Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates.bioRxiv : the preprint server for biology · 2023Article
- Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants.Frontiers in plant science · 2023Article
- A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use.PeerJ · 2022Article
- PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data.Applications in plant sciencesArticle
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Authors and funding
3 authors.
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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. The program is freely available at https://github.com/lmcai/PhyloHerb/. Conclusions: We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.
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