JTT.dcmut: The JTT.dcmut empirical amino acid substitution model

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Package:
Class JTT.dcmut

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralSubstitution
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AminoAcidSubst
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--JTT.dcmut

Directly known subclasses:

public static class JTT.dcmut
extends AminoAcidSubst

Usage

JTT.dcmut(equ.dist=NA, ...)

Arguments

equ.dist	Equilibrium distribution.
...	Not used.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AminoAcidSubst:
buildFromPAML, checkConsistency, newAAMatrix, setEquDist, 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

Author(s)

Botond Sipos, Gregory Jordan

References

Kosiol, C, and Goldman, N (2005) Different versions of the Dayhoff rate matrix - Molecular Biology and Evolution 22:193-199 http://dx.doi.org/10.1093/molbev/msi005

Jones, D. T., W. R. Taylor, and J. M. Thornton (1992) The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282 http://dx.doi.org/10.1093/bioinformatics/8.3.275

See Also

AminoAcidSubst GeneralSubstitution UNREST

Examples

	# create substitution model object
	p<-JTT.dcmut()
	# get object 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<-AminoAcidSequence(length=10,processes=list(list(p)) )
	# sample states
	sampleStates(s)
       # make the first threee positions invariable
       setRateMultipliers(s,p,0,1:3)
       # 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
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.