DAMBE pipeline

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

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Documentation


Maintainer


  • person_outline Xuhua Xia <>

Publications for Data Analysis for Molecular Biology and Evolution

DAMBE citations

 (17)
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 […]

2017
PMCID: 5562872

[…] studies1, 2, 11, were separately aligned according to amino sequence similarity by muscle implied in mega5 software47 and checked manually. then the aligned gene sequences were concatenated in dambe software48. all new sequences were submitted to genbank (supplementary table s2)., the time priors used in the divergence dating here are based on the following fossil dates: vanessa amerindica […]

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 […]

2016
PMCID: 4945904

[…] phylogenetic reconstruction. the extent of substitution saturation was estimated separately for entire codons and for the first, second, and third codon positions of the concatenated alignment using dambe51. the pairwise nucleotide differences (transitions and transversions) were plotted against the gtr genetic distance., the best-fit global model gtr+i+g was selected for the alignment of the 13 […]

2016
PMCID: 5240124

[…] saturation of bases was assessed using a graphic representation of transitions and transversions (ti-tv) plotted against kimura 2 parameters’ distance (kimura 1980). this analysis was run in dambe v. 5.3.105 (xia 2013)., pairwise comparisons of coi sequences were conducted for three categories: (i) individuals of the same species, (ii) individuals of the same genus (excluding […]

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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