Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering.

BioMed research international - 1 Jan 2014

Ilut Daniel C, Nydam Marie L, Hare Matthew P

Abstract excerpt

Next generation sequencing holds great promise for applications of phylogeography, landscape genetics, and population genomics in wild populations of nonmodel species, but the robustness of inferences hinges on careful experimental design and effective bioinformatic removal of predictable artifacts. Addressing this issue, we use published genomes from a tunicate, stickleback, and soybean to illustrate the...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Artifacts
Share to DNA Restriction Enzymes

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Share to Genome

Share to Glycine max

Share to Multigene Family

Share to Phylogeography

Share to Smegmamorpha

Share to Urochordata

Source

Open in PubMed Open full text

Identifiers

PMID: 25057498
DOI: 10.1155/2014/675158
PMCID: PMC4095725

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-08.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence. Graph snapshot: 2026-09-29.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering.PMID 25057498Read ↗

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage.Semantic proximity Read ↗

Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol.Semantic proximity Read ↗

Variant calling in nonmodel organisms with snpArcher.Semantic proximity Read ↗

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.Semantic proximity Read ↗

A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.Semantic proximity Read ↗

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations.Semantic proximity Read ↗

Allele identification in assembled genomic sequence datasets.Semantic proximity Read ↗

Genome-wide genetic marker discovery and genotyping using next-generation sequencing.Semantic proximity Read ↗

Estimating and accounting for genotyping errors in RAD-seq experiments.Semantic proximity Read ↗

Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.Semantic proximity Read ↗

Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication.Semantic proximity Read ↗

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.