ArticleApplications in plant sciences2016
HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.
Article in Applications in plant sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 296 papers.
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296 citing papers in PubMed, 841 citations in OpenAlex.
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- Upscaling Genotyping by Amplicon Sequencing With GBAS-GUI.Molecular ecology resources · 2026Article
- Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly.Nucleic acids research · 2026Article
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- Phasing Hyb-Seq loci from two combined bait sets to investigate phylogenetic patterns of hybridization within Boechera s.s. (Brassicaceae).Annals of botany · 2026Article
- Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae).Annals of botany · 2026Article
- A phylogenetic approach to prioritizing crop wild relatives in Brassiceae (Brassicaceae) for breeding applications.Annals of botany · 2026Article
- Murbeckiella is dead, long live Oreophyton: origin and systematics of tribe Oreophytoneae (Brassicaceae).Annals of botany · 2026Article
- Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family.Annals of botany · 2026Article
- Atlantic forest origins and Amazon connections: the evolutionary history of Adenocalymma.Annals of botany · 2026Article
- A tale of two lineages: comparative biogeography across the Southern Cone of two South American Carex (Cyperaceae) groups.Annals of botany · 2026Article
- A dataset of 352 nuclear genes for accurate species identification and geographical origin traceability ofData in brief · 2026Article
- Tracing Species Boundaries Through Genomic Baits: Diagnostic SNP Panels for Genotyping Orchid Pollinaria.Evolutionary applications · 2026Article
- Contrasting Dispersal Histories Shape Distinct Evolutionary Trajectories Between Malesian and PantropicalEcology and evolution · 2026Article
- Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding.Nature communications · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
236 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyUsing sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). METHODS AND
resultsHybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.
conclusionsHybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.