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Protocols

SIMMAP specifications

Information


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 citations

 (64)
library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] ew 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, and the n […]

call_split

Macroecology and macroevolution of the latitudinal diversity gradient in ants

2018
Nat Commun
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4
call_split See protocol

[…] ime-homogeneous 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 we recover […]

library_books

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

2018
BMC Evol Biol
PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] pled 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 Pr […]

call_split

Variation in social systems within Chaetodon butterflyfishes, with special reference to pair bonding

2018
PLoS One
PMCID: 5894994
PMID: 29641529
DOI: 10.1371/journal.pone.0194465
call_split See protocol

[…] ion 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 the s […]

call_split

Environmental determinism, and not interspecific competition, drives morphological variability in Australasian warblers (Acanthizidae)

2018
Ecol Evol
PMCID: 5916309
PMID: 29721264
DOI: 10.1002/ece3.3925
call_split See protocol

[…] s 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 (Revel […]

library_books

Anatomy of a Neotropical insect radiation

2018
BMC Evol Biol
PMCID: 5853117
PMID: 29540154
DOI: 10.1186/s12862-018-1146-9

[…] temporal 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 no polymor […]


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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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