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Protocols

DAMBE specifications

Information


Unique identifier OMICS_12355
Name DAMBE
Alternative names Data Analysis for Molecular Biology and Evolution, Dambe5, Dambe6
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format MEGA,PHYLIP,NEXUS,FASTA,NeXML
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 5.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Xuhua Xia

Publications for Data Analysis for Molecular Biology and Evolution

DAMBE citations

 (537)
library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] ment cleaning program GBlocks (implemented within TranslatorX) under the default parameters. Finally, the single alignments were concatenated into one data set, with a final length of 6,879 bp, using DAMBE 5.5.24.The datasets generated and/or analyzed in the current study are available from the corresponding author on request.All analyses were performed using data sets of both nucleotide (ND) and […]

call_split

Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

2018
PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0
call_split See protocol

[…] The frequencies of 16 dinucleotides per strain were calculated using DAMBE software. The ratio was calculated as follows:Pxy=rxyryrxwhere rx and ry represent the frequency of nucleotides X and Y, respectively, while rxy represents the observed dinucleotide XY value, an […]

call_split

Species Delimitation, Phylogenetic Relationships, and Temporal Divergence Model in the Genus Aeromonas

2018
Front Microbiol
PMCID: 5920023
PMID: 29731747
DOI: 10.3389/fmicb.2018.00770
call_split See protocol

[…] each gene, the translated sequences were aligned using the ClustalW program implemented in MEGA6 () and translated back to obtain the nucleotide alignments. Both alignments were concatenated with the DAMBE program (v5.3.10; ) and later the sequences were checked for the presence of incongruences or gaps. Divergent and ambiguously aligned blocks were also removed using the Gblocks program (). […]

call_split

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)

2018
BMC Genomics
PMCID: 5907366
PMID: 29669515
DOI: 10.1186/s12864-018-4650-9
call_split See protocol

[…] sequence similarity for all pairwise sequence comparisons. To test for substitution saturation, we plotted each codon position based on the K80 model for transition and transversion substitutions in DAMBE V4.5.32 [].The rate of non-synonymous substitutions (Ka), synonymous substitutions (Ks) and the ratio of Ka/Ks were calculated for each PCG in DnaSP 5.0 []. Estimated branch lengths were extract […]

library_books

Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China

2018
BMC Evol Biol
PMCID: 5894153
PMID: 29636000
DOI: 10.1186/s12862-018-1168-3

[…] g that mitochondrial DNA may experience substitution saturation because of its rapid evolutionary rate, we assessed substitution saturation using the test described by Xia et al. [] as implemented in DAMBE 6 (reference: Assessing substitution saturation with DAMBE) []. […]

call_split

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes)

2018
Front Genet
PMCID: 5893770
PMID: 29670644
DOI: 10.3389/fgene.2018.00107
call_split See protocol

[…] rochilodus) and 648 bp. To evaluate the occurrence of substitution saturation, the index of substitution saturation in asymmetrical (Iss.cAsym) and symmetrical (Iss.cSym) topologies were estimated in Dambe 5.3.38 (Xia, ). We used PartitionFinder 1.1.0 (Lanfear et al., ) to select the best-fit model of nucleotide evolution for our dataset.Species were previously identified following the most recent […]

Citations

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DAMBE institution(s)
University of Ottawa, Ottawa, ON, Canada
DAMBE funding source(s)
Supported by the Discovery Grant from Natural Science and Engineering Research Council (NSERC, RGPIN/261252) of Canada.

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