ArticleMolecular ecology2013
Stacks: an analysis tool set for population genomics.
Article in Molecular ecology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,594 papers.
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Who cites it
1,594 citing papers in PubMed.
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- Population Genomics of Almond (Prunus dulcis) Reveals Region-Specific Selection and a Complex History of Domestication.Molecular ecology · 2026Article
- Patterns of Evolutionary Diversification in a World-Significant Hotspot of Salmonid Diversity: A Study of LandlockedEcology and evolution · 2026Article
- Male-Biased Dispersal Leads to Expansion After Decline: The Hokkaido Brown Bear (Ecology and evolution · 2026Article
- Genotype-Phenotype-Environment Associations and Potential Local Adaptation Signals in the Mesquite Lizard Along the Eastern Trans-Mexican Volcanic Belt.Molecular ecology · 2026Article
1,534 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.