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A New Pipeline for Removing Paralogs in Target Enrichment Data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set
inferredcites →https://doi.org/10.1002/ece3.2623openalex-snapshot
Ecological genomics of local adaptation inCornus floridaL. by genotyping by sequencing
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Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.
inferredcites →https://doi.org/10.1007/978-1-4939-9074-0_5openalex-snapshot
Inferring Orthology and Paralogy
inferredcites →https://doi.org/10.1007/978-3-642-83962-7_18openalex-snapshot
DNA Protocols for Plants
inferredcites →https://doi.org/10.1007/s11295-006-0036-2openalex-snapshot
Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data
inferredcites →https://doi.org/10.1016/j.gdata.2016.05.012openalex-snapshot
Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip
inferredcites →https://doi.org/10.1016/j.jtbi.2010.09.010openalex-snapshot
Sampling-through-time in birth–death trees
inferredcites →https://doi.org/10.1016/j.pbi.2013.11.002openalex-snapshot
Gene duplication as a driver of plant morphogenetic evolution
inferredcites →https://doi.org/10.1016/j.tplants.2019.07.011openalex-snapshot
Hyb-Seq for Flowering Plant Systematics
inferredcites →https://doi.org/10.1016/j.ympev.2006.07.022openalex-snapshot
Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America
inferredcites →https://doi.org/10.1016/j.ympev.2010.02.018openalex-snapshot
Evolution and biogeographic diversification of the witch-hazel genus (Hamamelis L., Hamamelidaceae) in the Northern Hemisphere
inferredcites →https://doi.org/10.1016/j.ympev.2011.12.007openalex-snapshot
Applications of next-generation sequencing to phylogeography and phylogenetics
inferredcites →https://doi.org/10.1016/j.ympev.2019.106601openalex-snapshot
Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous
inferredcites →https://doi.org/10.1016/j.ympev.2019.106668openalex-snapshot
A phylogenomic analysis of Nepenthes (Nepenthaceae)
inferredcites →https://doi.org/10.1016/j.ympev.2019.106726openalex-snapshot
Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0305-1978(98)00067-2openalex-snapshot
A phylogenetic and biogeographic study of Hamamelis (Hamamelidaceae), an eastern Asian and eastern North American disjunct genus
inferredcites →https://doi.org/10.1038/hdy.2012.79openalex-snapshot
Polyploidy and its effect on evolutionary success: old questions revisited with new tools
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1038/s41586-019-1693-2openalex-snapshot
One thousand plant transcriptomes and the phylogenomics of green plants
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu121openalex-snapshot
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btv646openalex-snapshot
PHYLUCE is a software package for the analysis of conserved genomic loci
inferredcites →https://doi.org/10.1093/bioinformatics/btz966openalex-snapshot
ipyrad: Interactive assembly and analysis of RADseq datasets
inferredcites →https://doi.org/10.1093/gbe/evr115openalex-snapshot
Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications
inferredcites →https://doi.org/10.1093/gbe/evv026openalex-snapshot
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/mss162openalex-snapshot
Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
UFBoot2: Improving the Ultrafast Bootstrap Approximation
inferredcites →https://doi.org/10.1093/molbev/msy194openalex-snapshot
Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree
inferredcites →https://doi.org/10.1093/sysbio/syr025openalex-snapshot
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syr087openalex-snapshot
Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syw036openalex-snapshot
Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics
inferredcites →https://doi.org/10.1093/sysbio/syx050openalex-snapshot
Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syy021openalex-snapshot
Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data
inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
inferredcites →https://doi.org/10.1093/sysbio/syy086openalex-snapshot
A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
inferredcites →https://doi.org/10.1093/sysbio/syz074openalex-snapshot
Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris)
inferredcites →https://doi.org/10.1099/mgen.0.000122openalex-snapshot
Aligner optimization increases accuracy and decreases compute times in multi-species sequence data
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
inferredcites →https://doi.org/10.1111/1442-1984.12196openalex-snapshot
Genetic structure of the clonal herb Tanakaea radicans (Saxifragaceae) at multiple spatial scales, revealed by nuclear and mitochondrial microsatellite markers
inferredcites →https://doi.org/10.1111/1755-0998.12613openalex-snapshot
Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping‐by‐sequencing data from natural populations
inferredcites →https://doi.org/10.1111/cobi.12380openalex-snapshot
Estimating the normal background rate of species extinction
inferredcites →https://doi.org/10.1111/j.1365-294x.1992.tb00182.xopenalex-snapshot
Design and testing of a plant‐specific PCR primer for ecological and evolutionary studies
inferredcites →https://doi.org/10.1111/j.1558-5646.1998.tb01828.xopenalex-snapshot
ORIGIN AND BIOGEOGRAPHY OF AESCULUS L. (HIPPOCASTANACEAE): A MOLECULAR PHYLOGENETIC PERSPECTIVE
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02967.xopenalex-snapshot
Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
inferredcites →https://doi.org/10.1111/jse.12516openalex-snapshot
Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma
inferredcites →https://doi.org/10.1111/jse.12599openalex-snapshot
Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North AmericanNyssa(Nyssaceae)
inferredcites →https://doi.org/10.1111/jse.12646openalex-snapshot
Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
inferredcites →https://doi.org/10.1111/mec.13601openalex-snapshot
Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135822openalex-snapshot
High-Throughput Genomic Data in Systematics and Phylogenetics
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0065923openalex-snapshot
A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
inferredcites →https://doi.org/10.1371/journal.pone.0104008openalex-snapshot
Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach
inferredcites →https://doi.org/10.1534/g3.120.401532openalex-snapshot
Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome
inferredcites →https://doi.org/10.3389/fpls.2019.01655openalex-snapshot
Tackling Rapid Radiations With Targeted Sequencing
inferredcites →https://doi.org/10.3389/fpls.2020.00258openalex-snapshot
Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics
inferredcites →https://doi.org/10.3732/apps.1400042openalex-snapshot
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
inferredcites →https://doi.org/10.3732/apps.1600016openalex-snapshot
HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
inferredcites →https://doi.org/10.4137/ebo.s9627openalex-snapshot
Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets
inferredcites →https://doi.org/10.5962/bhl.title.2293openalex-snapshot
Studies of American plants. VII
inferredcites →https://doi.org/10.5962/p.324752openalex-snapshot
Revision of Castanea Sect. Balanocastanon (Fagaceae)
inferredcites →https://doi.org/10.7554/elife.45199openalex-snapshot
Natural selection and repeated patterns of molecular evolution following allopatric divergence
inferredcites →https://doi.org/10.7717/peerj.5175openalex-snapshot
SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.3897/phytokeys.251.136373zenodo-depositor-declared
Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae)
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An updated phylogeny, biogeography, and PhyloCode‐based classification of Cornaceae based on three sets of genomic data
inferred← citeshttps://doi.org/10.1002/aps3.11537openalex-snapshot
Target capture and genome skimming for plant diversity studies
inferred← citeshttps://doi.org/10.1002/aps3.11568openalex-snapshot
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems
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A roadmap of phylogenomic methods for studying polyploid plant genera
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From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?
inferred← citeshttps://doi.org/10.1007/s44281-023-00026-zopenalex-snapshot
Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107592openalex-snapshot
Phylogenomics AND biogeography of Castanea (chestnut) and Hamamelis (witch-hazel) – Choosing between RAD-seq and Hyb-Seq approaches
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107826openalex-snapshot
REFMAKER: Make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108239openalex-snapshot
Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing − A case study with planktonic ciliates (Ciliophora, Oligotrichea)
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Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand
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Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108703openalex-snapshot
Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae)
inferred← citeshttps://doi.org/10.1038/s41598-024-72622-6openalex-snapshot
Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales
inferred← citeshttps://doi.org/10.1071/sb24011openalex-snapshot
Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data
inferred← citeshttps://doi.org/10.1093/aob/mcad047openalex-snapshot
Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae)
inferred← citeshttps://doi.org/10.1093/aob/mcaf128openalex-snapshot
Resolving relationships in the radiation of Australia’s largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad332openalex-snapshot
Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies
inferred← citeshttps://doi.org/10.1093/botlinnean/boad022openalex-snapshot
Target capture sequencing for phylogenomic and population studies in the Southeast Asian genusPalaquium(Sapotaceae)
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Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae
inferred← citeshttps://doi.org/10.1093/molbev/msac261openalex-snapshot
Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research
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Rampant Reticulation in a Rapid Radiation of Tropical Trees—Insights from Inga (Fabaceae)
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Phylogenetic reconstruction and taxonomy of Retinella land snails: congruence and conflicts across morphological, mitochondrial, and nuclear datasets
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Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems
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Rampant Reticulation in a Rapid Radiation of Tropical Trees - Insights from Inga (Fabaceae)
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ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications
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Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
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GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data
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Upscaling Genotyping by Amplicon Sequencing With GBAS ‐ GUI
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Ecological and Evolutionary Factors Contribute to the Uneven Diversification of Firs in the Northern Hemisphere
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Dispersal and in Situ Speciation as Contributors to Plant Diversity in the Chocó Region: Insights From Inga Mill. (Leguminosae)
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Phylogenomics and the flowering plant tree of life
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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
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Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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A family‐level phylogeny of liverworts (Marchantiophyta): New insights from mitochondrial sequences
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Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars
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Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan
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Resolving Phylogenetic Relationships of a Recently and Rapidly Evolving Lineage from Western North America (Mentzelia Section Bartonia, Loasaceae)
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Structural haplotypes act as supergene-like additive units that mitigate the genomic prediction cliff in mango
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Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)
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Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species – influences of host identity, environment, phylogeny, and geographic isolation
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Organellar phylogenomics of Ophioglossaceae fern genera
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ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits in Salicornia spp.
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A new nanofibre derived from Trichoderma hamatum K01 to control durian rot caused by Phytophthora palmivora
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Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics
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A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome
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Evolutionary relationships and allied species of Pyronemataceae, with segregation of the novel family Pyropyxidaceae
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Peer Review #1 of "A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.14525v0.1/reviews/2openalex-snapshot
Peer Review #2 of "A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.14525v0.2/reviews/2openalex-snapshot
Peer Review #2 of "A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.14525v0.3/reviews/2openalex-snapshot
Peer Review #2 of "A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use (v0.3)"
inferred← citeshttps://doi.org/10.7717/peerj.14525openalex-snapshot
A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
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