DensityMap statistics

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DensityMap specifications


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
Maintained Yes


  • Primates
    • Homo sapiens



  • person_outline Yves Bigot

Publication for DensityMap

DensityMap citations


The baubellum is more developmentally and evolutionarily labile than the baculum

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

[…] tions 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 (, available upon request. Branches where a transition occurred in at least 50% of the […]


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

Nat Commun
PMCID: 5431902
PMID: 28232746
DOI: 10.1038/s41467-016-0012-y
call_split See protocol

[…] e 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 of characte […]


Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms

Front Genet
PMCID: 4288051
PMID: 25620977
DOI: 10.3389/fgene.2014.00452
call_split See protocol

[…] eing the transition matrix between both states. This was achieved using the use.empirical = TRUE option in make.simmap. We undertook 10,000 generations sampling every 100 steps. We used the function ‘DensityMap’ in Phytools to depict the changes in posterior probabilities (PP) along branches of the phylogeny. […]


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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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