Population Genetic Software For Mac
R-package program to detect markers responding to selection. Renaud VITALIS. Linux - Windows - Mac.
The program structure is a free software package for usingmulti-locus genotype data to investigate population structure. Itsuses include inferring the presence of distinct populations, assigningindividuals to populations, studying hybrid zones, identifyingmigrants and admixed individuals, and estimating population allelefrequencies in situations where many individuals are migrants oradmixed. It can be applied to most of the commonly-used geneticmarkers, including SNPS, microsatellites, RFLPs and AFLPs.
In 2016 John Novembre wrote a short historical perspective of Structure.
DownloadStructure 2.3.4.
fastSTRUCTURE for large SNP datasets is out now! Links to the preprint and software (beta release) by Anil, Matthew and Jonathan.
What to cite: The basic algorithm was described by Pritchard, Stephens & Donnelly (2000). Extensions to the method were published by Falush,Stephens and Pritchard (2003),and (2007)and Hubisz, Falush, Stephens and Pritchard (2009).
Contributors: Daniel Falush,Melissa Hubisz, Matthew Stephens, Jonathan Pritchard, Peter Donnelly, William Wen, Mike Trienis, Pall Melsted.
Questions and Discussion: There is a Structurediscussion forum to which you can directquestions. Many thanks to Vikram Chhatre who moderatesthis discussion group. Bug Reports.
Plotting programs and other resources: The Structure software performs basic plotting and reporting of results. CLUMPAK byNaama Kopelman and Itay Mayrose builds on Noah Rosenberg's earlier programsCLUMPP and distruct forproducing nice graphical displays of structureresults, and computing useful statistics. StructureHarvester by Dent Earl provides additional tools for visualizing Structure output. Xavier Didelot's program xmfa2structconverts files in eXtended Multi-Fasta (XMFA) formatinto Structure input format.
Genome-wide SNP data:TreeMix by Joe Pickrelland Jonathan uses large numbers of SNPs to estimate thehistorical relationships among populations, using agraph representation that allows both population splits and migrationevents. [Note: Joe's latest release now allows microsat data too.] fastSTRUCTUREby Anil Raj, Matthew and Jonathan, for running Structure on very large SNP datasets [Raj et al 2014].fineSTRUCTURE by DanielLawson and colleagues enables analyses of very fine scalestructure for genome-wide SNP data.
Sample data sets: available here.
Taita thrush: An example of MCMCconvergence based on the original paper is shown here.
Some miscellaneous applications:structure has been widely used for interpreting populationstructure of humans and other organisms. A selection of interestingreferences (mainly applications) is shown below.
Traces of human migrations in Helicobacter pylori populations. D. Falush,T. Wirth, B. Linz, J.K. Pritchard, M. Stephens and 13 others, 2003. Science,299: 1582-1585. [PDF]
The genetic structure of human populations. N.A. Rosenberg,J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd,L.A. Zhivotovsky and M.W. Feldman, 2002. Science, 298:2381-2385. (and technical comment, 2003) [PDF]
Dwarf8 polymorphisms associate with variation in flowering time. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES.Nat Genet. 2001 28:286-9. [PubMed Abstract]
Apogee duet 2 usb 2.0 audio interface for mac pro. The drivers for this unit are a little confusing. I find if my computer goes to sleep, the duet freezes up and has to be reset, that's a little annoying. I do have the Protools version.
Origin of extant domesticated sunflowers in eastern North America.Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA, Rieseberg LH.Nature. 2004 430:201-5. [PubMed Abstract]
Emerging vectors in the Culex pipiens complex. Fonseca DM,Keyghobadi N, Malcolm CA, Mehmet C, Schaffner F, Mogi M, Fleischer RC,Wilkerson RC. Science. 2004 303:1535-8. [PubMed Abstract]
Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds.Rosenberg NA et al. Genetics. 2001 159:699-713. [PubMed Abstract]