DnaSP protocols

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DnaSP specifications

Information


Unique identifier OMICS_01820
Name DnaSP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for DnaSP

DnaSP in pipelines

 (445)
2018
PMCID: 5759284
PMID: 29310678
DOI: 10.1186/s12977-017-0383-0

[…] that encode the entire mature gp51 are derived from an 804 bp restriction fragment that does not contain signal peptide coding sequence., the following steps were performed during the meme and dnasp analysis. first, a multiple sequence alignment was generated using clustalw implemented in geneious pro 5.5.9 software (biomatters ltd). second, the aligned sequences were submitted to the meme […]

2018
PMCID: 5764299
PMID: 29386908
DOI: 10.2147/IDR.S152162

[…] were designated as “new”. new allele sequences and the allelic profiles of novel sts were submitted to the p. aeruginosa mlst data-base for assignment of the correct allelic numbers and sts., dnasp v5 was used to analyze the genetic variability at mlst loci for the 160 isolated strains. the mean g+c content, polymorphic sites, difference in number of nucleotides, […]

2018
PMCID: 5765603
PMID: 29325573
DOI: 10.1186/s12936-018-2176-x

[…] in thailand (n = 33), myanmar (n = 8), and lao pdr (n = 4), using conventional polymerase chain reaction (pcr) assay. then, the pcr products were sequenced and analysed using bioedit, mega6, and dnasp programs., the average pairwise nucleotide diversities (π) of p. malariae trap, ama1, and p48/45 were 0.00169, 0.00413, and 0.00029, respectively. the haplotype diversities (hd) of p. malariae […]

2018
PMCID: 5773674
PMID: 29348510
DOI: 10.1038/s41598-018-19169-5

[…] pc170, we investigated the positive selection signal (dn/ds > 1) using codeml (with m0 model) implemented in paml, version 4.8. for the 32 positively selected secreted genes, we then performed dnasp, version 5.10.1 and kaks_calculator 2.0 to calculate the dn/ds values, and these results supported the codeml calculations., the pc170 strain was grown on potato dextrose agar. the mycelia […]

2018
PMCID: 5783425
PMID: 29324738
DOI: 10.1371/journal.pntd.0006165

[…] structure of ribosomal dna sequences. the nucleotide composition, conserved sites, variable sites, parsimony-informative sites, and singleton sites were estimated using mega v.6.06., the program dnasp v5.10 [] was employed to analyze the number of haplotypes, haplotype diversity (hd), and nucleotide diversity (pi) of each molecular marker. network v5.0 [] was used to draw a median-joining […]

DnaSP in publications

 (2295)
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] 16 plant species were downloaded from phytozome (http://phytozome.jgi.doe.gov/pz/portal.html) (table ). ka and ks values were calculated for two gene pairs, smdml2/smdml3 and smdml5/smdml6, using dnasp5 software., total rna was isolated from s. miltiorrhiza tissues using the plant total rna extraction kit (aidlab, china). the isolation was carried out following the manufacturer’s […]

PMCID: 5930942
PMID: 29716645
DOI: 10.1186/s13071-018-2847-z

[…] haplotypes with some close relationship to the waterbird haplotypes described in the present study., haemosporidian diversity indices were determined for each waterbird population using the dnasp program, version 5 []. diversity indices (gene or haplotype diversity [] and nucleotide diversity []) were evaluated by their variances as well as using a statistical test comparing gene […]

PMCID: 5932820
PMID: 29720181
DOI: 10.1186/s12936-018-2337-y

[…] was used to align dna sequences []. bioedit v7 was used to calculate sequences identity []. analysis of haplotype and nucleotide diversity was performed by using dnasp v5 []. the nei’s unbiased expected heterozygosity (he) was calculated as a measure of overall genetic diversity for each genotype method []. analysis of molecular variance (amova) was conducted […]

PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] as fasta with bcftools version 1.6 []. the resulting sequences where aligned using clustal omega [], the alignment was checked and trimmed in phyde version 0.9971 []. calculations were done using dnasp version 6.10.03 [], vcftools version 0.1.15 [] and microsoft excel 2016., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: additional file 6: […]

PMCID: 5920075
PMID: 29700348
DOI: 10.1038/s41598-018-24585-8

[…] (tcs) using popart to assess genealogical relationships between the global pfcsp haplotypes found in pf3k and the haplotypes from zambia and the drc,. genetic diversity metrics were calculated using dnasp (version 6.10.01). we compared sequences between african and asian countries in terms of diversity and for evidence of population differentiation by calculating fst. similarly, we compared […]

DnaSP institution(s)
Departament de Genètica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain

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