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DensityMap specifications

Information


Unique identifier OMICS_11756
Name DensityMap
Interface Web user interface
Restrictions to use None
Input data Sequences and sequences regions
Input format GFF3 and BED
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Source code URL https://codeload.github.com/sguizard/DensityMap/zip/master
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Yves Bigot

Publication for DensityMap

DensityMap citations

 (4)
library_books

Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions

2018
Front Plant Sci
PMCID: 5818461
PMID: 29497436
DOI: 10.3389/fpls.2018.00175

[…] the centromeric regions annotation was performed using repeatmasker (–div 20 option) and edited with artemis, and transposable elements density along genomic sequences was carried out using densitymap (guizard et al., )., seedlings of c. arabica, c. canephora, and c. eugenioides were obtained from the agronomic institute of paraná (iapar), londrina, paraná, brazil, cultivated in pots […]

library_books

The baubellum is more developmentally and evolutionarily labile than the baculum

2017
Ecol Evol
PMCID: 5773289
PMID: 29375780
DOI: 10.1002/ece3.3634

[…] of stochastic mapping across each of the four strategies described above, using only the 163 species for which both baculum and baubellum were scored. visual representations were made using the densitymap function of phytools (revell, ), as well as customized scripts written in r (https://www.r-project.org), available upon request. branches where a transition occurred in at least 50% […]

library_books

Repeated evolution of soldier sub castes suggests parasitism drives social complexity in stingless bees

2017
Nat Commun
PMCID: 5431902
PMID: 28232746
DOI: 10.1038/s41467-016-0012-y

[…] posterior density of stochastically mapped character history was plotted on the phylogeny (fig. ). the visualization of the aggregate result of the 1,000 stochastic maps was done using the function densitymap of the r phylogenetics package phytools. maximum likelihood and parsimony reconstructions were also run, mainly to evaluate the influence of branch lengths on the interpretation […]

library_books

Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

2016
BMC Genomics
PMCID: 4992247
PMID: 27542599
DOI: 10.1186/s12864-016-3015-5

[…] et chimie du vivant” of the universitary pres centre val de loire. peter arensburger holds a senior researcher fellowship from studium., all custom written gff files and software (gfftools and densitymap.pl) are available at http://chicken-repeats.inra.fr/index.php?pages/tools., sg, bp and yb designed the research program; sg, bp and yb performed the analyses; sg, pa, fg and yb wrote […]


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DensityMap institution(s)
UMR INRA-CNRS 7247, China, Centre INRA Val de Loire, France
DensityMap funding source(s)
This work was funded by the Région Centre (AviGeS Project), C.N.R.S., I.N.R.A., the Groupements de Recherche CNRS 3546 (Elements Génétiques Mobiles) and 3604 (Modèles Aviaires), and the Ministère de l’Education Nationale, de la Recherche et de la Technologie.

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