Description Usage Arguments Fields and Methods Author(s) References See Also Examples
This class implements the F81 GTR-submodel.
Package:
Class F81
Object
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PSRoot
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Process
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GeneralSubstitution
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UNREST
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GTR
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F81
Directly known subclasses:
public static class F81
extends GTR
1 |
name |
Object name. |
base.freqs |
Base frequency parameters. |
... |
Not used. |
Methods:
checkConsistency | - | |
getBaseFreqs | - | |
getRateParam | - | |
getRateParamList | - | |
setBaseFreqs | - | |
setRateParam | - | |
setRateParamList | - | |
summary | - | |
Methods inherited from GTR:
checkConsistency, getBaseFreqs, getRateParam, getRateParamList, setBaseFreqs, setRateParam, setRateParamList, summary
Methods inherited from UNREST:
checkConsistency, summary
Methods inherited from GeneralSubstitution:
as.character, checkConsistency, clone, getAlphabet, getEquDist, getEventRate, getEventRateAtSite, getEventsAtSite, getQMatrix, getRate, getRateList, hasUndefinedRate, is, plot, rescaleQMatrix, sampleState, setAlphabet, setEquDist, setQMatrix, setRate, setRateList, summary
Methods inherited from Process:
!=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, setWriteProtected, summary
Methods inherited from PSRoot:
checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Botond Sipos, Gregory Jordan
Felsenstein, J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach - Journal of Molecular Evolution 17:368-376 http://dx.doi.org/10.1007/BF01734359
GTR UNREST GeneralSubstitution HKY
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | # create substitution process object
p<-F81(base.freqs=c(1,2,3,4)/10)
# get a summary
summary(p)
# display a bubble plot
plot(p)
# The following code demonstrates how to use
# the process in a simulation.
# create a sequence, attach process p
s<-NucleotideSequence(length=20,processes=list(list(p)))
# sample states
sampleStates(s)
# make the first five positions invariable
setRateMultipliers(s,p,0,1:5)
# get rate multipliers
getRateMultipliers(s,p)
# create a simulation object
sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
# run simulation
Simulate(sim)
# print alignment
sim$alignment
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