DAMBE specifications

Information


Unique identifier OMICS_12355
Name DAMBE
Alternative name Data Analysis for Molecular Biology and Evolution
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

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Documentation


Maintainer


  • person_outline Xuhua Xia <>

DAMBE articles

DAMBE citations

 (12)
2017
PMCID: 5493672

[…] using the nei-gojobori method68 as implemented in mega7 software69, with default settings., to estimate the level of substitution saturation, we used the approach of xia et al.70 as implemented in dambe5 software71. the amount of substitutional saturation was calculated for four scenarios: the first codon position, the second codon position, the combined the first and the second codon […]

2016
PMCID: 5004829

[…] dedham, massachusetts, usa). sequences were aligned using the clustal w interface with the mega 5 software (tamura et al., 2011). the saturation levels of the molecular data were determined using dambe software version 5.0.39 (xia and xie, 2001). transition and transversion were plotted based on the tn93 model from each gene data set (tamura and nei, 1993). distance estimates of genetic […]

2016
PMCID: 4911057

[…] using the software sequencescanner (applied biosystems) and bioedit [27]. alignment and curation of sequences was done with the program mega 5.2 [28] and clustalw. sequences were concatenated with dambe 5.3.9 [29] and mega 5.2 was used to construct a neighbor-joining tree with standard settings. the pairwise deletion option was used to treat missing data and gaps; finally the tree was tested […]

2016
PMCID: 4836724

[…] concatenated into a supermatrix., to test for potential substitutional saturation [89, 90] the index of substitutional saturation statistic was calculated for the supermatrix (test implemented in dambe version 6.0.0 [91]). the results indicated that the observed saturation index of 0.5865 was smaller than the critical saturation index (iss.c = 0.8023), suggesting that the sequences […]

2015
PMCID: 4608823

[…] success using bm and bcm is 100%., a neighbor-joining (nj) tree [37] (using k2p distances) and a maximum likelihood (ml) tree [38] were constructed after removing identical sequences with dambe v.5 [39]. we focused on whether individuals of the same species clustered together, rather than on the evolutionary relationships between species (i.e. tree-based identification sensu [13,14], […]

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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