DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

By Pablo Librado, Julio Rozas. Bioinform., 2009

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View Paper: https://www.semanticscholar.org/paper/05e25b9797de9a544ca50e743aa2a15eb129ea72

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In Genetics

Citations in the corpus

Species distribution models and mitochondrial DNA phylogeography suggest an extensive biogeographical shift in the high‐intertidal seaweed Pelvetia canaliculata (2014, methodology): “Haplotype (Hhap) and nucleotide diversities (phap) within populations and selected geographical regions were calculated with DnaSP 5 (Librado & Rozas, 2009).”
Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China (2017, methodology): “Chloroplast haplotypes were identified with DnaSP 5 (Librado & Rozas, 2009) and a haplotype network was constructed using network 4.6.11 with the median-joining model (Bandelt et al., 1999).”
Glacial expansion and diversification of an East Asian montane bird, the green‐backed tit (Parus monticolus) (2013, methodology): “The McDonald–Kreitman test (McDonald & Kreitman, 1991) implemented in DnaSP 5.0 (Librado & Rozas, 2009) was used to examine the selective neutrality of the three mitochondrial coding fragments by comparing the polymorphism within the green-backed tit to that in the great tit.”
Phylogeography and climatic niche evolution in live oaks (Quercus series Virentes) from the tropics to the temperate zone (2011, methodology): “Sequences were tested for deviance from neutrality 966 Journal of Biogeography 38, 962–981 ª 2011 Blackwell Publishing Ltd using Tajima’s D in DnaSP 5.0 (Librado & Rozas, 2009), but none showed significant deviance.”
Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene (2011, methodology): “Tajima_s D, Fay and Wu_s H, and McDonald–Kreitman tests were performed with DNAsp (Librado and Rozas 2009).”
Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: study of a Neotropical fish of the Brazilian coastal Atlantic Forest (2015, methodology): “Standard population genetic summaries were calculated for each population and palaeodrainages using DnaSP (Librado & Rozas, 2009) and Arlequin 3.5 (Excoffier & Lischer, 2010).”
A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications (2014, methodology): “InDels and parsimony informative sites were detected using DnaSp v 5.10.01 (Librado & Rozas 2009), and InDels were treated as a fifth character in phylogenetic analyses.”
New primers for the amplification and sequencing of nuclear loci in a taxonomically wide set of reptiles and amphibians (2010, methodology): “00.7 (Librado and Rozas 2009) for polymorphism analysis.”
Population Demography and Genetic Diversity in the Pleistocene Cave Lion (2015, methodology): “0 (Librado and Rozas, 2009) on three partitions of the dataset (control region; ATP8; both markers merged).”
Multiple introductions and invasion pathways for the invasive ctenophore Mnemiopsis leidyi in Eurasia (2011, methodology): “To test neutral evolution of the marker, we calculated Tajima’s D (Tajima 1989), and Fu and Li’s (1993) D*, using DnaSP version 5 (Librado and Rozas 2009).”
popart: full‐feature software for haplotype network construction (2015, methodology): “…software packages that are no longer maintained ( TCS ) or are available for either Microsoft Windows (e.g. ARLEQUIN , Excoﬃer, Laval & Schneider 2005; NET-WORK ; DNASP , Librado & Rozas 2009) or Mac OS X (e.g. GENODIVE , http://www.bentleydrummer.nl/software/software/ GenoDive.html), but not both.”
Tracing the origin of US brown marmorated stink bugs, Halyomorpha halys (2013, methodology): “Population genetic diversity, as indexed by the number of haplotypes (Hn), haplotype diversity (Hd) and nucleotide diversity (hp), was assessed with DnaSP 5.0 (Librado and Rozas 2009).”