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SIMMAP specifications

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Unique identifier OMICS_23385
Name SIMMAP
Alternative name StochastIc Mutational MApping on Phylogenies
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS
License SIMMAP Free Academic End-user License
Computer skills Medium
Version 1.5
Stability Stable
Maintained No

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Publication for StochastIc Mutational MApping on Phylogenies

SIMMAP in pipelines

 (5)
2018
PMCID: 5916309
PMID: 29721264
DOI: 10.1002/ece3.3925

[…] were run across a sample of 100 trees obtained from the posterior distribution of the bayesian analysis. for the multi‐peak (oum) models, we first built stochastic character‐mapped reconstructions (simmap; bollback, ) of (1) foraging niche categories, (2) regions, and (3) adaptive peaks estimated by surface, for each of the 100 trees sampled from the posterior distribution, using phytools […]

2015
PMCID: 4357287
PMID: 25650739
DOI: 10.7554/eLife.05463.018

[…] the eu morph per treatment per species is reported in for pooled samples., to infer the evolutionary history of the stomatal dimorphism, we used stochastic character mapping (; ) as implemented in simmap 1.5 (). this approach estimates probabilities of the states along phylogeny under continuous-time markov models, incorporating uncertainty in tree topology, branch length, and ancestral […]

2014
PMCID: 4010409
PMID: 24798481
DOI: 10.1371/journal.pone.0095722

[…] using the harmonic-mean estimator ., using the maximum-clade-credibility trees from our bayesian analyses, we inferred the number of substitutions at each site using stochastic mutational mapping in simmap , . we used the empirical nucleotide frequencies and applied the mean rate estimate from the bayesian phylogenetic analysis of each data set to scale the branch lengths. numbers were rounded […]

2010
PMCID: 2880065
PMID: 20053660
DOI: 10.1098/rsbl.2009.0989

[…] to the classification of growth habitats of anguilliform fishes of , the ancestral growth habitats in anguilliforms were reconstructed using ml and bayesian approaches using mesquite v. 2.6 () and simmap v.1.0 beta 2.4 (), respectively. four discrete character states were assigned to the growth habitats of the terminal nodes: shallow water (character state 0), outer shelf and slope (state 1), […]

2007
PMCID: 2000896
PMID: 17692128
DOI: 10.1186/1471-2148-7-136

[…] the independent contrast method., we also tested character associations between discrete characters of sociality and tonal sound complexity using two different methods. first we used the software simmap 1.0 [] which allows for multistate character associations. we did the following tests using all post-burnin trees (n = 2000) from our bayesian analysis (may-collado et al. 2007) [] using […]


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SIMMAP in publications

 (58)
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] transition rate matrix was sampled from the posterior distribution of each model in proportion to the calculated akaike weights. we generated 1000 character histories for each model using the make.simmap command and summarized the results using describe.simmap to determine the posterior probabilities that each internal node is at each state, the proportion of time spent in each state, […]

PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4

[…] models, we crosschecked the marginal ancestral state probabilities from diversitree with marginal probabilities calculated from stochastic character mapping simulations using the make.simmap function in the r package phytools, and found them to be identical aside from sampling noise. we also performed a resampling procedure to evaluate whether the ancestral state pattern […]

PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] trees using the prune function in phyutility [] and reran bpcomp on both chains., we conducted character-mapping analyses under the explicit statistical models for character evolution described in simmap and implemented in phytools [, , ]. simmap uses stochastic character mapping to simulate the evolution of characters on a posterior distribution of trees, resulting in estimates of posterior […]

PMCID: 5894994
PMID: 29641529
DOI: 10.1371/journal.pone.0194465

[…] rates among sociality character states and highlight the temporal origins of group sizes. to begin, we ran 1000 stochastic character maps on the mcc tree of cowman and bellwood [] using the ‘make.simmap’ function of phytools with q = “mcmc” to sample the transition matrix (q) from its posterior probability distribution. the mean transition matrix from this analysis was then used to infer […]

PMCID: 5853117
PMID: 29540154
DOI: 10.1186/s12862-018-1146-9

[…] extremes of the possible timing of character transformations. additionally, we investigated whether patterns varied across the phylogeny by analyzing splits separately for clades a, b and c., simmap results were tallied for each of the 2500 simulated reconstructions and summarized using a custom r script. this process was more straightforward, as individual simulations contained […]


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SIMMAP institution(s)
Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
SIMMAP funding source(s)
Supported by grants from NSF (MCB-0075404), grants from NIH and Danish FNU, and a grant from the Danish FNU.

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