mtMam: The mtMam empirical amino acid substitution model

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Package:
Class mtMam

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralSubstitution
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AminoAcidSubst
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--mtMam

Directly known subclasses:

public static class mtMam
extends AminoAcidSubst

Usage

mtMam(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

Yang, Z., R. Nielsen, and M. Hasegawa (1998) Models of amino acid substitution and applications to Mitochondrial protein evolution, Molecular Biology and Evolution 15:1600-1611 http://bit.ly/by4NMb

See Also

AminoAcidSubst GeneralSubstitution UNREST

Examples

	# create substitution model object
	p<-mtMam()
	# 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 three 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.