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orthoCapture: Facilitating Gene Capture Probe Design for Non-Model Species

https://doi.org/10.1101/703942
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics
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Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms
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Biotic Interactions, Rapid Evolution, and the Establishment of Introduced Species
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FLASH: fast length adjustment of short reads to improve genome assemblies
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COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt593openalex-snapshot
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
inferredcites →https://doi.org/10.1093/gbe/evx005openalex-snapshot
Targeted capture of complete coding regions across divergent species
inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msv216openalex-snapshot
An Exon-Capture System for the Entire Class Ophiuroidea
inferredcites →https://doi.org/10.1093/molbev/msw056openalex-snapshot
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkg033openalex-snapshot
Database resources of the National Center for Biotechnology
inferredcites →https://doi.org/10.1093/nar/gkx1095openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gkx1098openalex-snapshot
Ensembl 2018
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/10.1098/rstb.2011.0198openalex-snapshot
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing
inferredcites →https://doi.org/10.1101/361618openalex-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/10.1101/gr.121327.111openalex-snapshot
Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection
inferredcites →https://doi.org/10.1111/1755-0998.12059openalex-snapshot
Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics
inferredcites →https://doi.org/10.1111/1755-0998.12222openalex-snapshot
A targeted next‐generation sequencing toolkit for exon‐based cichlid phylogenomics
inferredcites →https://doi.org/10.1111/1755-0998.12449openalex-snapshot
Exon capture phylogenomics: efficacy across scales of divergence
inferredcites →https://doi.org/10.1111/1755-0998.12487openalex-snapshot
Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
inferredcites →https://doi.org/10.1111/1755-0998.12541openalex-snapshot
An evaluation of transcriptome‐based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
inferredcites →https://doi.org/10.1111/1755-0998.12552openalex-snapshot
Identification and qualification of 500 nuclear, single‐copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
inferredcites →https://doi.org/10.1111/1755-0998.12905openalex-snapshot
Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms
inferredcites →https://doi.org/10.1111/2041-210x.12754openalex-snapshot
Identifying conserved genomic elements and designing universal bait sets to enrich them
inferredcites →https://doi.org/10.1111/mec.13304openalex-snapshot
Targeted capture in evolutionary and ecological genomics
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2164-12-347openalex-snapshot
Exome-wide DNA capture and next generation sequencing in domestic and wild species
inferredcites →https://doi.org/10.1186/1471-2164-13-403openalex-snapshot
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
inferredcites →https://doi.org/10.1186/gb-2011-12-9-r87openalex-snapshot
Expanding whole exome resequencing into non-human primates
inferredcites →https://doi.org/10.1371/journal.pone.0067908openalex-snapshot
Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time
inferredcites →https://doi.org/10.3732/apps.1300085openalex-snapshot
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae
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.1400115openalex-snapshot
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes
inferredcites →https://doi.org/10.7717/peerj.3569openalex-snapshot
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
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