/AminoAcidMatrices.R
http://github.com/sbotond/phylosim · R · 942 lines · 165 code · 49 blank · 728 comment · 0 complexity · 13d32c17283616ebfc6ed0ae0ff30201 MD5 · raw file
- ##
- ## Copyright 2009 Botond Sipos
- ## See the package description for licensing information.
- ##
- ## cpREV
- ##
- ##########################################################################/**
- #
- # @RdocClass cpREV
- #
- # @title "The cpREV empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa (2000) Plastid
- # genome phylogeny and a model of amino acid substitution for proteins
- # encoded by chloroplast DNA - Journal of Molecular Evolution 50:348--358
- # DOI: 10.1007/s002399910038 \url{http://bit.ly/bnBVLm}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-cpREV()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "cpREV",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="cpREV",
- paml.file="cpREV.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## PAM
- ##
- ##########################################################################/**
- #
- # @RdocClass PAM
- #
- # @title "The PAM empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Dayhoff, M. O.; Schwartz, R. M.; Orcutt, B. C. (1978). "A model of evolutionary change in proteins" -
- # Atlas of Protein Sequence and Structure 5 (3):345-352
- #
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-PAM()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "PAM",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="PAM",
- paml.file="dayhoff.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## PAM-dcmut
- ##
- ##########################################################################/**
- #
- # @RdocClass PAM.dcmut
- #
- # @title "The PAM.dcmut empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Kosiol, C, and Goldman, N (2005) Different versions of the Dayhoff rate matrix -
- # Molecular Biology and Evolution 22:193-199 \url{http://dx.doi.org/10.1093/molbev/msi005}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-PAM.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 three 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "PAM.dcmut",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="PAM.dcmut",
- paml.file="dayhoff-dcmut.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## JTT
- ##
- ##########################################################################/**
- #
- # @RdocClass JTT
- #
- # @title "The JTT empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # 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 \url{http://dx.doi.org/10.1093/bioinformatics/8.3.275}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-JTT()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "JTT",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="JTT",
- paml.file="jones.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## JTT.dcmut
- ##
- ##########################################################################/**
- #
- # @RdocClass JTT.dcmut
- #
- # @title "The JTT.dcmut empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Kosiol, C, and Goldman, N (2005) Different versions of the Dayhoff rate matrix -
- # Molecular Biology and Evolution 22:193-199 \url{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 \url{http://dx.doi.org/10.1093/bioinformatics/8.3.275}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "JTT.dcmut",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="JTT.dcmut",
- paml.file="jones-dcmut.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## LG
- ##
- ##########################################################################/**
- #
- # @RdocClass LG
- #
- # @title "The LG empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Le, S. Q., and O. Gascuel (2008) An improved general amino acid replacement matrix -
- # Mol. Biol. Evol. 25:1307-1320 \url{http://dx.doi.org/10.1093/molbev/msn067}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-LG()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "LG",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="LG",
- paml.file="lg.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## mtArt
- ##
- ##########################################################################/**
- #
- # @RdocClass mtArt
- #
- # @title "The mtArt empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Abascal, F., D. Posada, and R. Zardoya (2007) MtArt: A new Model of
- # amino acid replacement for Arthropoda - Mol. Biol. Evol. 24:1-5 \url{http://dx.doi.org/10.1093/molbev/msl136}
- #
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-mtArt()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "mtArt",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="mtArt",
- paml.file="mtArt.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## mtMam
- ##
- ##########################################################################/**
- #
- # @RdocClass mtMam
- #
- # @title "The mtMam empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \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 \url{http://bit.ly/by4NMb}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "mtMam",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="mtMam",
- paml.file="mtmam.dat",
- equ.dist=equ.dist
- );
-
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## mtREV24
- ##
- ##########################################################################/**
- #
- # @RdocClass mtREV24
- #
- # @title "The mtREV24 empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Adachi, J. and Hasegawa, M. (1996) MOLPHY version 2.3: programs for
- # molecular phylogenetics based on maximum likelihood. Computer Science
- # Monographs of Institute of Statistical Mathematics 28:1-150
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-mtREV24()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "mtREV24",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="mtREV24",
- paml.file="mtREV24.dat",
- equ.dist=equ.dist
- );
-
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## MtZoa
- ##
- ##########################################################################/**
- #
- # @RdocClass MtZoa
- #
- # @title "The MtZoa empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Rota-Stabelli, O., Z. Yang, and M. Telford. (2009) MtZoa: a general mitochondrial amino acid
- # substitutions model for animal evolutionary studies. Mol. Phyl. Evol 52(1):268-72 \url{http://bit.ly/bjZfKi}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-MtZoa()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "MtZoa",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="MtZoa",
- paml.file="MtZoa.dat",
- equ.dist=equ.dist
- );
-
- return(this);
- },
- enforceRCC=FALSE
- );
- ##
- ## WAG
- ##
- ##########################################################################/**
- #
- # @RdocClass WAG
- #
- # @title "The WAG empirical amino acid substitution model"
- #
- # \description{
- #
- #
- # @classhierarchy
- # }
- #
- # \references{
- # Whelan, S. and N. Goldman (2001) A general empirical model of
- # protein evolution derived from multiple protein families using a maximum likelihood
- # approach - Molecular Biology and Evolution 18:691-699 \url{http://bit.ly/dpTKAd}
- # }
- #
- # @synopsis
- #
- # \arguments{
- # \item{equ.dist}{Equilibrium distribution.}
- # \item{...}{Not used.}
- # }
- #
- # \section{Fields and Methods}{
- # @allmethods
- # }
- #
- # \examples{
- # # create substitution model object
- # p<-WAG()
- # # 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$alignment
- # }
- #
- # @author
- #
- # \seealso{
- # AminoAcidSubst GeneralSubstitution UNREST
- # }
- #
- #*/###########################################################################
- setConstructorS3(
- "WAG",
- function(
- equ.dist=NA,
- ...
- ){
- this<-AminoAcidSubst$newAAMatrix(
- name="WAG",
- paml.file="wag.dat",
- equ.dist=equ.dist
- );
- return(this);
- },
- enforceRCC=FALSE
- );