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Stacks | Building and genotyping Loci de novo from short-read sequences

Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core population genomic summary statistics and single nucleotide polymorphism (SNP)-by-SNP statistical tests. It aims to be a key resource to empower researchers to efficiently perform ecological and evolutionary genomic studies in model organisms and particularly in organisms with minimal or no genomic resources.

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Stacks forum

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Stacks classification

Stacks specifications

Unique identifier:
OMICS_01567
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 2.0
Version:
1.4.6
Maintained:
Yes
Software type:
Package/Module, Pipeline/Workflow
Restrictions to use:
None
Programming languages:
C++, Perl
Computer skills:
Advanced
Stability:
Stable

Stacks distribution

versioning

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Stacks classification

Stacks specifications

Unique identifier:
OMICS_01567
Restrictions to use:
None
Stability:
Stable
Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes

Stacks distribution

download

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Stacks classification

Stacks specifications

Unique identifier:
OMICS_01567
Restrictions to use:
None
Maintained:
Yes
Software type:
Pipeline/Workflow
Stability:
Stable

Stacks distribution

download

Stacks support

Documentation

Maintainer

  • William Cresko <>
  • William Cresko <>
  • William Cresko <>

Credits

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Publications

Institution(s)

Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA; Biological Sciences, University of Idaho, Moscow, ID, USA; Institute of Neuroscience, University of Oregon, Eugene, OR, USA

Funding source(s)

Supported by NSF grants IOS-1027283, DEB-0949053 (WAC), NIH grant 1R24GM079486-01A1, the M. J. Murdock Charitable Trust, NIH NRSA Ruth L. Kirschstein fellowship F32GM095213-01 and NIH NCRR grant P20RR16448.

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