| Released | Last version | Language | OS | Supported alignment formats | Supported SNP data formats | |
|---|---|---|---|---|---|---|
| DnaSP | 1995 | 5.10.1 (2010/03) | Visual Basic | MS Windows | FASTA, MEGA, NBRF/PIR, NEXUS, PHYLIP | HapMap |
| PAML | 1997 | 4.8a (2014/08) | ANSI C | UNIX/Linux, MAC OSX, MS Windows | PHYLIP, NEXUS (limited support) | — |
| LAMARC | 2001 | 2.1.10 (2016/01) | C++ | UNIX/Linux, MAC OSX, MS Windows | PHYLIP, (own) | (own) |
| Arlequin | 2005 | 3.5.2.2 (2015/08) | C++, R | UNIX/Linux, MAC OSX, MS Windows | (own) | (own) |
| VariScan | 2005 | 2.0.3 (2012/07) | C++ | UNIX/Linux, MAC OSX, MS Windows | MAF, MGA, XMFA, PHYLIP | HapMap |
| PLINK | 2007 | 1.9 beta 3.38 (2016/06), 1.07 stable (2009/10) | C/C++ | UNIX/Linux, MAC OSX, MS Windows | — | PED/MAP (own) |
| adegenet and pegas | 2008; 2010 | Adegenet, 2.0.1 (2016/02); Pegas, 0.9 (2016/04) | R | UNIX/Linux, MAC OSX, MS Windows | FASTA, NEXUS, PHYLIP, (own) | VCF, FSTAT, GENETIX, GENEPOP, STRUCTURE, (own) |
| PopGenome | 2014 | 2.1.6 (2015/05) | R | UNIX/Linux, MAC OSX, MS Windows | FASTA, NEXUS, MEGA, MAF, PHYLIP, RData, (own) | VCF, SNP, HapMap, MS, MSMS |
| ANGSD | 2014 | 0.911 (2016/03) | C/C++ | UNIX/Linux | BAM, CRAM, MPILEUP | VCF, GLF, BEAGLE |
DnaSP, http://www.ub.edu/dnasp/ (Rozas and Rozas 1995, 1997, 1999; Rozas et al. 2003; Librado and Rozas 2009; Rozas 2009); PAML, http://abacus.gene.ucl.ac.uk/software/paml.html (Yang 1997, 2007); LAMARC, http://evolution.genetics.washington.edu/lamarc/index.html (Kuhner 2006; Kuhner and Smith 2007); Arlequin, http://cmpg.unibe.ch/software/arlequin35 (Excoffier et al. 2005; Excoffier and Lischer 2010); VariScan, http://www.ub.edu/softevol/variscan (Vilella et al. 2005; Hutter et al. 2006); PLINK, http://pngu.mgh.harvard.edu/∼purcell/plink/ (Purcell et al. 2007); adegenet, http://adegenet.r-forge.r-project.org/ (Jombart 2008; Jombart and Ahmed 2011); pegas, http://ape-package.ird.fr/pegas.html (Paradis 2010); PopGenome, http://popgenome.weebly.com/ (Pfeifer et al. 2014); and ANGSD, http://www.popgen.dk/angsd (Korneliussen et al. 2014).