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Protocols

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 citations

 (6)
call_split

Molecular and Cytogenetic Characterization of Wild Musa Species

2015
PLoS One
PMCID: 4529165
PMID: 26252482
DOI: 10.1371/journal.pone.0134096
call_split See protocol

[…] using 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 […]

library_books

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis

2015
Genome Biol Evol
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). […]

library_books

Mapping by Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

2014
Genetics
PMCID: 4174949
PMID: 24996910
DOI: 10.1534/genetics.114.165613

[…] r 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 (). […]

library_books

Detecting Selection in the Blue Crab, Callinectes sapidus, Using DNA Sequence Data from Multiple Nuclear Protein Coding Genes

2014
PLoS One
PMCID: 4045945
PMID: 24896825
DOI: 10.1371/journal.pone.0099081

[…] lity 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, the […]

library_books

Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers

2013
PLoS Genet
PMCID: 3854799
PMID: 24339787
DOI: 10.1371/journal.pgen.1003965

[…] istical 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 tha […]

library_books

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests

2012
Evol Appl
PMCID: 3492901
PMID: 23144662
DOI: 10.1111/j.1752-4571.2012.00256.x

[…] Aligned sequences were analyzed with the DNA Sequence Analysis and Manipulation (DnaSAM) program (). Sites with missing data, with indels, or that violated the infinite sites mutational model were not included in the analysis. For each gene, […]


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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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