Table 1. Selected Population Genetics Programs.
| Program | Functions | Platform | Update | Authors | URL |
|---|---|---|---|---|---|
| Admixture | Clustering | Windows | 2015 | Alexander etal. |
https://www.genetics.ucla.edu/software/admixture/ |
| Arlequin (123) †‡ |
HWE, Fst, AMOVA |
Windows Mac Linux |
2015 | Excoffier, and Lischer |
http://cmpg.unibe.ch/software/arlequin35/ |
| Bottleneck (127) † |
Expected heterozygosity |
Windows | 1999 | Cornuet et al. | http://www1.montpellier.inra.fr/CBGP/software/Bottleneck/bottleneck.html |
| diveRsity | HWE, Fst, Ar | R package | 2017 | Keenan | http://diversityinlife.weebly.com/ |
| DnaSP (124) ‡ |
Fst, Gst | Windows Mac Linux |
2018 | J. Rozas et al. | http://www.ub.edu/dnasp/ |
| estMOl (30) |
Haplotype generation |
Windows | 2014 | Assefa et al. | http://pathogenseq.lshtm.ac.uk |
| Fluctuate‡ | Ne | Windows Mac Linux |
2002 | Kuhner | http://evolution.genetics.washington.edu/lamarc.html |
| FSTAT | HWE, Fst, Rst | Windows | 2005 | J Goudet | http://www2.unil.ch/popgen/softwares/fstat.htm |
| Genealex (121) † |
HWE, Ae, Fst, Rst, Gst, G’st, Jost’s D, Nm and AMOVA |
Windows Mac |
2016 | Peakall and Smouse |
http://biology-assets.anu.edu.au/GenAIEx/ |
| Genepop (122) |
HWE, Nm, Fst* |
Online Windows Mac Linux Unix |
2017 | Raymond and Rousset |
http://genepop.curtin.edu.au/ |
| Genetix | HWE, Fst, Gst | Windows | 2004 | K Belkhir., etal. | http://kimura.univmontp2.fr/genetix/ |
| MLNE (126) † |
Ne, m, Nm | Windows | 2003 | Wang | https://www.zsl.org/science/software/mine |
| mmod (129) |
Dest, G”ST and φ’ST |
R package | 2017 | Winter et al. | https://github.com/dwinter/mmod |
| Pegas (130) |
HWE, Fst, AMOVA |
R package | 2017 | Paradis | https://cran.r-project.org/web/packages/pegas/index.html |
| Popgen (131) |
HWE, Ar | R package | 2016 | Kamvar | http://popgen.nescent.org/ |
| PopGen Report (128) |
HWE, summary statistics, Dest, G”st and φ’st |
R package | 2015 | Adamack and Gruber |
http://www.popgenreport.org/ |
| Poptree2 (113) |
GST, standardized GST, and Jost’s D |
Online, Windows, DOS, UNIX |
2014 | N. Takezaki, M. Nei, and K. Tamura |
http://www.med.kagawa-u.ac.jp/~genomelb/takezaki/poptree2/index.html |
| SpadeR† | Jost’s D | Online R package |
2015 | Chao | http://chao.stat.nthu.edu.tw/wordpress/ |
| SPAGeDi (125) |
Fst, Gst, Rst | Windows Mac Linux |
2015 | Hardy and Vekemans |
http://ebe.ulb.ac.be/ebe/SPAGeDi.html |
| Structure (96) |
Clustering | Windows Mac |
2012 | Pritchard et al. | http://web.stanford.edu/group/pritchardlab/structure.html |
| TFPGA | HWE, Fst, genetic distance |
Windows | 2000 | Miller | http://www.marksgeneticsoftware.net/tfpga.htm |
Most programs perform additional analyses, but the emphasis here is for measures of differentiation and diversity discussed in this part. All programs accept discrete genotypes, except DnaSP. Some (†) accept allele frequency data and others (‡) raw DNA sequences. Programs producing estimates of Fst using Weir and Cockerham (121) are indicated by (*). Additional lists of programs can be found in Excoffier et al. (33) or at websites:
- Population genetics in R (http://grunwaldlab.github.io/Population_Genetics_in_R/)
- University of Washington (https://courses.washington.edu/popgen/Software.htm)
- Softlinks (http://softlinks.amnh.org/popgen.html)