DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software).DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. Moreover, DnaSP can conduct a number of neutrality tests, such as (among other), the Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997), Ramos-Onsins and Rozas (2002), Achaz (2009) tests, and compute their confidence intervals by the coalescent. The results of the analyses are displayed on tabular and graphic form.Input Data Files:A single MSA (one genomic region) in a number of file formats such as FASTA, NEXUS, MEGA, NBRF, PHYLIP, etc. [from version 1]A single MSA storing DNA sequence information (haplotype) along with their frequency, in ARP format (Excoffier and Lischer 2010) [version 6 and newer]A multi-MSA File in *.alleles, *.loci and *.fa file formats (generated by PyRAD and STACKS softwares; -Eaton et al. 2014; Catchen et al. 2013), as well as VCF formats (Danecek et al. 2011) [version 6 and newer]
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