New Publication: Stacks Software for Population Genomics in Molecular Ecology
We’re excited to announce a new publication in Molecular Ecology describing major advances in the Stacks software package for population genomics!
Led by Dr. Julian Catchen with contributions from Paul Hohenlohe, Susan Bassham, and Bill Cresko, this paper presents powerful new extensions to the Stacks software that enable efficient analysis of genotype-by-sequencing data for population genomic studies. These tools are transforming how researchers worldwide study natural populations.
About Stacks
Stacks is an open-source software pipeline for: - Processing RAD-seq and related genotyping-by-sequencing data - Identifying SNPs and genotypes in non-model organisms - Calculating population genomic statistics - Conducting phylogeographic analyses - Managing large-scale genomic datasets
New Capabilities
The publication describes major enhancements including: - Population genomic summary statistics calculations - SNP-by-SNP statistical tests - Improved algorithms for genotype calling - Scalability for large datasets - Integration with downstream analysis tools
Research Impact
Stacks has become essential infrastructure for: - Conservation genomics projects - Evolutionary biology studies - Agricultural genomics - Ecological genetics research - Phylogeographic analyses
Global Adoption
Since its release, Stacks has: - Been downloaded thousands of times - Enabled hundreds of published studies - Supported research on diverse organisms - Democratized population genomics - Advanced the field of molecular ecology
Collaborative Development
This software represents collaboration between: - Julian Catchen (now at University of Illinois) - Paul Hohenlohe (now at University of Idaho) - Susan Bassham (University of Oregon) - William Cresko (University of Oregon) - The global RAD-seq community
Technical Innovation
Stacks addresses key challenges in: - Handling massive sequencing datasets - Accounting for sequencing errors - Identifying paralogs - Population structure analysis - Comparative genomics
Open Science
The Stacks project exemplifies open science through: - Free and open-source code - Comprehensive documentation - Active user community - Regular updates and improvements - Transparent development process
Training and Support
We provide extensive resources including: - Detailed tutorials - Workshop materials - User forums - Regular updates - Technical support