Reference health
HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
1 of 36 checkable references need attention · checked 2026-09-23
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
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References needing attention
does not resolve to a known work10.1111/1755‐0998.12449
The 35 checked references that resolve
resolves10.1089/cmb.2012.0021
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
resolves10.1186/1471-2164-13-403
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
resolves10.1186/s12862-015-0318-0
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
resolves10.1093/bioinformatics/btp348
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
resolves10.1093/bioinformatics/btp163
Biopython: freely available Python tools for computational molecular biology and bioinformatics
resolves10.1093/bioinformatics/btv646
PHYLUCE is a software package for the analysis of conserved genomic loci
resolves10.1093/sysbio/sys004
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
resolves10.3732/apps.1500039
A protocol for targeted enrichment of intron‐containing sequence markers for recent radiations: A phylogenomic example from <i>Heuchera</i> (Saxifragaceae)
resolves10.3732/apps.1600017
Low‐coverage, whole‐genome sequencing of <i>Artocarpus camansi</i> (Moraceae) for phylogenetic marker development and gene discovery
resolves10.1093/sysbio/syv029
The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
resolves10.1038/nbt.1523
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
resolves10.1093/molbev/mst010
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
resolves10.1093/bioinformatics/btp324
Fast and accurate short read alignment with Burrows–Wheeler transform
resolves10.3732/apps.1300085
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae
resolves10.1093/sysbio/syw005
Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:<i>Piranga</i>)
resolves10.1111/1755-0998.12258
Cost‐effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
resolves10.1098/rspb.2015.1413
Replicated divergence in cichlid radiations mirrors a major vertebrate innovation
resolves10.1038/nature12130
Inferring ancient divergences requires genes with strong phylogenetic signals
resolves10.1093/sysbio/syt061
Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
resolves10.1093/bioinformatics/btu033
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
resolves10.3732/ajb.1500031
Species tree estimation of diploid <i>Helianthus</i> (Asteraceae) using target enrichment
resolves10.1186/1471-2164-12-211
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing
resolves10.3732/apps.1200497
A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
resolves10.3732/apps.1400042
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
resolves10.1600/036364410X539853
Phylogeny and Recircumscription of Artocarpeae (Moraceae) with a Focus on <I>Artocarpus</I>
The 1 reference without a DOI — listed, not checked
no DOI — not checkedGNU Parallel: The Command‐Line Power Tool
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