DnaSAM statistics

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DnaSAM specifications

Information


Unique identifier OMICS_25408
Name DnaSAM
Alternative name DNA Sequence Analysis and Manipulation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An alignment file.
Input format FASTA
Output data A tab-limited text file with statistics and relevant P-values.
Output format TXT
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained No

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Publication for DNA Sequence Analysis and Manipulation

DnaSAM in publications

 (6)
PMCID: 4529165
PMID: 26252482
DOI: 10.1371/journal.pone.0134096

[…] staden package []. sequence boundaries of the spacers were assessed and phylogenetic relationships analysis was performed according to hřibová et al. []. sequence diversity was identified using dnasam program [] with 1000 simulations. splitstree4 v4.1.11 [] was used to construct phylograms based on the jukes-cantor model. non-parametric bootstrapping with 1000 pseudoreplicates was performed […]

PMCID: 4453061
PMID: 25888688
DOI: 10.1093/gbe/evv066

[…] by the gene being present at the end of an assembled contiguous sequence. for each of these core genes, we calculated the watterson’s estimator of population mutation rate () and tajima’s d () using dnasam (). the overall distribution of estimators for each gene and each species were compared using a mann–whitney u test (wilcoxon’s rank sum test)., trees were constructed based on 2,059 core s. […]

PMCID: 4174949
PMID: 24996910
DOI: 10.1534/genetics.114.165613

[…] for biotechnology information (ncbi) genbank (dq201145, dq201146, and dq238106). haplotype analysis was performed as described in . nucleotide diversity π was calculated for the coding region using dnasam v. 20100621 ()., positions of the gaf and pas domains at hvphyc were determined using interproscan (). a set of 4419 protein sequences of the phy homologs from plant and bacterial species […]

PMCID: 4045945
PMID: 24896825
DOI: 10.1371/journal.pone.0099081

[…] tests, departures from neutral expectations were detected with tajima's d , fay and wu's normalized h , and the ewens-watterson ew homozygosity test . significance of all tests was determined in dnasam using 103 simulations that assumed a neutral model and no recombination. because d, h, and ew differ in their sensitivities to demographic history, background selection, and recombination, […]

PMCID: 3854799
PMID: 24339787
DOI: 10.1371/journal.pgen.1003965

[…] support for these cutoffs we generated 10,000 replicate datasets for each ptp in the upper and lower 2.5% tails of the distribution under a neutral model in the ms program implemented in the dnasam computer package with default simulation parameters . p-values were calculated for each of these loci as the proportion of 10,000 coalescent simulations with a tajima's d value more extreme […]


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DnaSAM institution(s)
Section of Evolution and Ecology, University of California at Davis, Davis, CA, USA; Center for Population Biology, University of California at Davis, Davis, CA, USA; Department of Plant Sciences, University of California at Davis, Davis, CA, USA
DnaSAM funding source(s)
Supported by NSF grant DBI-0501763.

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