Table 2 Selection of software available for population genetics/genomics analyses
ReleasedLast versionLanguageOSSupported alignment formatsSupported SNP data formats
DnaSP19955.10.1 (2010/03)Visual BasicMS WindowsFASTA, MEGA, NBRF/PIR, NEXUS, PHYLIPHapMap
PAML19974.8a (2014/08)ANSI CUNIX/Linux, MAC OSX, MS WindowsPHYLIP, NEXUS (limited support)
LAMARC20012.1.10 (2016/01)C++UNIX/Linux, MAC OSX, MS WindowsPHYLIP, (own)(own)
Arlequin20053.5.2.2 (2015/08)C++, RUNIX/Linux, MAC OSX, MS Windows(own)(own)
VariScan20052.0.3 (2012/07)C++UNIX/Linux, MAC OSX, MS WindowsMAF, MGA, XMFA, PHYLIPHapMap
PLINK20071.9 beta 3.38 (2016/06), 1.07 stable (2009/10)C/C++UNIX/Linux, MAC OSX, MS WindowsPED/MAP (own)
adegenet and pegas2008; 2010Adegenet, 2.0.1 (2016/02); Pegas, 0.9 (2016/04)RUNIX/Linux, MAC OSX, MS WindowsFASTA, NEXUS, PHYLIP, (own)VCF, FSTAT, GENETIX, GENEPOP, STRUCTURE, (own)
PopGenome20142.1.6 (2015/05)RUNIX/Linux, MAC OSX, MS WindowsFASTA, NEXUS, MEGA, MAF, PHYLIP, RData, (own)VCF, SNP, HapMap, MS, MSMS
ANGSD20140.911 (2016/03)C/C++UNIX/LinuxBAM, CRAM, MPILEUPVCF, GLF, BEAGLE