DnaSP

Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio, Sara Guirao-Rico, Pablo Librado, Sebastián Ramos-Onsins and Alejandro Sánchez-Gracia
Universitat de Barcelona
Current Beta Version: 6.12.03 (February 26, 2019)

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]

    New features in DnaSP in v6 | DnaSP User-Interface | Running DnaSP under Windows, Linux and MacIntosh | Known Bugs in v6 | Source Code |

    Go To DnaSP version 5 (version 5.10.1 -March 2009)

    DnaSP version 6 for 32-bit and 64-bit environments (ZIP file of 11.7 Mb)

    Download DnaSP v6

    DnaSP v6 Documentation (PDF)

    The installation of the 64-bit version (x64) requires a 64-bit based processor and OS (nearly all computers acquired in the last decade are based in this architecture). Since almost all computers should work with the 64-bit version, it is better to install the most powerful 64-bit version. If it does not work, try the 32-bit one (x86).


    References:

    • Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., Sánchez-Gracia, A. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 34: 3299-3302. DOI: 10.1093/molbev/msx248

    • Librado, P. and Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.

    • Rozas, J. (2009). DNA Sequence Polymorphism Analysis using DnaSP. Pp. 337-350. In Posada, D. (ed.) Bioinformatics for DNA Sequence Analysis; Methods in Molecular Biology Series Vol. 537. Humana Press, NJ, USA.

    • Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X. and Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.

    • Rozas, J. and Rozas, R. (1999). DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.

    • Rozas, J. and Rozas, R. (1997). DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. Comput. Applic. Biosci. 13: 307-311.

    • Rozas, J. and Rozas, R. (1995). DnaSP, DNA sequence polymorphism: an interactive program for estimating Population Genetics parameters from DNA sequence data. Comput. Applic. Biosci. 11: 621-625.

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    Accesses since January 2017