Julio Rozas et al. 2017
Universitat de Barcelona
DnaSP Version 6.0 (2017)
New features included in DnaSP version 6:
Migration of the DnaSP software from VB 6.0 to VB.NET.
Computer optimization using multithreading.
Computing new neutrality tests, such as the Y and Y* of Achaz (2008), and the E from Zeng et al. (2006).
Increasing the capabilities of the previous batch mode to automatically read and analyse (intraspecific and interespecific variation) multiple data files sequentially.
Analysis of RADseq and hybrid enrichment-based data. DnaSP can read and interpret Multi-MSA file formats, such as the *.alleles, *.loci and *.fa file formats, generated by PyRAD and STACKS programs (Eaton et al. 2014, Catchen et al. 2013), as well as the popular Variant Calling Format (VCF) (Danecek et al. 2011). Therefore, the software provides compatibility with standard NGS (next generation sequencing) pipelines. DnaSP v6 can perform diverse comprehensive population genetics-based analyses, depending on the information provided as input data. Indeed, many relevant statistics that in DnaSP v5 were only available under the single-loci mode, can be now estimated from Multi-MSA files. These summary statistics include the levels and patterns of DNA sequence variation within and between populations, the levels of linkage disequilibrium and gene flow (for different ploidy levels), and a number of neutrality tests.
Possibility of estimating the observed heterozygosity levels across individuals (for genotype data).
Analysis of haplotype-frequency data files with hundreds of thousands DNA sequences. DnaSP can read and interpret the Arlequin file formata (*.arp; Excoffier and Lischer 2010) storing DNA sequence information (haplotype) along with their frequency. The outcome of these analyses include nucleotide-based and haplotype-based summary statistics within and between samples, and across groups (populations).
Extensively expanded the capabilities to analyse data under the coalescent, by implementing methods and algorithms described in Hudson (2002) and Ramos-Onsins and Mitchell-Olds (2007). The new coalescent DnaSP v6 module automatically reads the summary statistics calculated from either a single locus or multilocus data, the latter calculated using new batch mode feature. Moreover, v6 also allows conducting coalescent simulations under the standard neutral model, but also under other demographic scenarios, including population growth, decline, bottleneck, and split/admixture, enable then to contrast the fit of different models to the data, by means of their p-values and/or confidence intervals.
Modification of many windows displaying the results in form of graphs.
And many other features.