Harnessing the power of RADseq for ecological and evolutionary genomics
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq)
are enabling the low-cost discovery and genotyping of thousands of genetic markers for any …
are enabling the low-cost discovery and genotyping of thousands of genetic markers for any …
Applications of genotyping by sequencing in aquaculture breeding and genetics
Selective breeding is increasingly recognized as a key component of sustainable production
of aquaculture species. The uptake of genomic technology in aquaculture breeding has …
of aquaculture species. The uptake of genomic technology in aquaculture breeding has …
ipyrad: Interactive assembly and analysis of RADseq datasets
DAR Eaton, I Overcast - Bioinformatics, 2020 - academic.oup.com
Abstract Summary ipyrad is a free and open source tool for assembling and analyzing
restriction site-associated DNA sequence datasets using de novo and/or reference-based …
restriction site-associated DNA sequence datasets using de novo and/or reference-based …
DnaSP 6: DNA sequence polymorphism analysis of large data sets
J Rozas, A Ferrer-Mata… - Molecular biology …, 2017 - academic.oup.com
We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version
of the popular tool for performing exhaustive population genetic analyses on multiple …
of the popular tool for performing exhaustive population genetic analyses on multiple …
Deriving genotypes from RAD-seq short-read data using Stacks
NC Rochette, JM Catchen - Nature Protocols, 2017 - nature.com
Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …
Genomic landscape of the global oak phylogeny
The tree of life is highly reticulate, with the history of population divergence emerging from
populations of gene phylogenies that reflect histories of introgression, lineage sorting and …
populations of gene phylogenies that reflect histories of introgression, lineage sorting and …
Minor allele frequency thresholds strongly affect population structure inference with genomic data sets
E Linck, CJ Battey - Molecular Ecology Resources, 2019 - Wiley Online Library
A common method of minimizing errors in large DNA sequence data sets is to drop variable
sites with a minor allele frequency (MAF) below some specified threshold. Although …
sites with a minor allele frequency (MAF) below some specified threshold. Although …
Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference
Restriction site‐associated DNA sequencing (RAD‐seq) provides high‐resolution
population genomic data at low cost, and has become an important component in ecological …
population genomic data at low cost, and has become an important component in ecological …
These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists
Sequencing reduced‐representation libraries of restriction site‐associated DNA (RAD seq)
to identify single nucleotide polymorphisms (SNP s) is quickly becoming a standard …
to identify single nucleotide polymorphisms (SNP s) is quickly becoming a standard …
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Restriction site‐associated DNA sequencing (RAD seq) provides researchers with the ability
to record genetic polymorphism across thousands of loci for nonmodel organisms …
to record genetic polymorphism across thousands of loci for nonmodel organisms …