$	extract-methods
$,AutomorphismList-method	extract-methods
aaindex2	aaindex2
aaindex3	aaindex3
aa_mutmat	aa_mutmat
aln	aln
as.AutomorphismList	as.AutomorphismList
as.AutomorphismList,GRangesList,GRanges_OR_NULL-method	as.AutomorphismList
as.AutomorphismList,list,GRanges_OR_NULL-method	as.AutomorphismList
as.list,AutomorphismList-method	AutomorphismList
aut3D	aut3D
autby_coef	autby_coef
autm	autm
autm_3d	autm_3d
autm_z125	autm_z125
Automorphism	Automorphism
Automorphism-class	Automorphism
AutomorphismByCoef	AutomorphismByCoef
AutomorphismByCoef-class	AutomorphismByCoef
AutomorphismByCoefList	AutomorphismByCoefList
AutomorphismByCoefList-class	AutomorphismByCoefList
automorphismByRanges	automorphismByRanges
automorphismByRanges,Automorphism-method	automorphismByRanges
automorphismByRanges,AutomorphismList-method	automorphismByRanges
AutomorphismList	AutomorphismList
AutomorphismList-class	AutomorphismList
AutomorphismList-methods	extract-methods
automorphisms	automorphisms
automorphisms,DNAStringSet_OR_NULL-method	automorphisms
automorphism_bycoef	automorphism_bycoef
automorphism_bycoef,Automorphism-method	automorphism_bycoef
automorphism_bycoef,AutomorphismList-method	automorphism_bycoef
autZ125	autZ125
autZ5	autZ5
autZ64	autZ64
base2codon	base2codon
base2codon,character-method	base2codon
base2codon,DNAMultipleAlignment-method	base2codon
base2codon,DNAStringSet-method	base2codon
base2int	base2int
base2int,character-method	base2int
base2int,data.frame-method	base2int
BaseGroup	BaseGroup
BaseGroup-class	BaseGroup
BaseGroup_OR_CodonGroup	BaseGroup_OR_CodonGroup
BaseGroup_OR_CodonGroup-class	BaseGroup_OR_CodonGroup
base_coord	base_coord
base_coord,DNAStringSet_OR_NULL-method	base_coord
base_repl	base_repl
brca1_aln	brca1_aln
brca1_aln2	brca1_aln2
brca1_autm	brca1_autm
brca1_autm2	brca1_autm2
CodonGroup	CodonGroup
CodonGroup-class	CodonGroup
CodonSeq	CodonSeq
CodonSeq-class	CodonSeq
codon_coord	codon_coord
codon_coord,BaseGroup-method	codon_coord
codon_coord,DNAStringSet_OR_NULL-method	codon_coord
codon_coord,matrix_OR_data_frame-method	codon_coord
ConservedRegion	ConservedRegion
ConservedRegion-class	ConservedRegion
ConservedRegionList	ConservedRegion
ConservedRegionList-class	ConservedRegion
conserved_regions	conserved_regions
conserved_regions,Automorphism-method	conserved_regions
conserved_regions,AutomorphismByCoef-method	conserved_regions
conserved_regions,AutomorphismByCoefList-method	conserved_regions
conserved_regions,AutomorphismList-method	conserved_regions
coordList	CodonSeq
coordList,CodonSeq-method	CodonSeq
covid_aln	covid_aln
covid_autm	covid_autm
cyc_aln	cyc_aln
cyc_autm	cyc_autm
DataFrame_OR_data.frame-class	Automorphism
DNAStringSet	reexports
DNAStringSet_OR_NULL-class	valid.MatrixList
end	reexports
end<-	reexports
GenomAutomorphism	GenomAutomorphism
getAutomorphisms	getAutomorphisms
getAutomorphisms,AutomorphismList-method	getAutomorphisms
getAutomorphisms,DataFrame_OR_data.frame-method	getAutomorphisms
getAutomorphisms,list-method	getAutomorphisms
get_coord	get_coord
get_coord,BaseGroup_OR_CodonGroup-method	get_coord
get_coord,DNAStringSet_OR_NULL-method	get_coord
get_mutscore	get_mutscore
get_mutscore,character,character-method	get_mutscore
GRangesList	reexports
GRanges_OR_NULL-class	GRanges_OR_NULL
is.url	is.url
matrices	matrices
matrices,CodonSeq-method	matrices
matrices,DNAStringSet_OR_NULL-method	matrices
matrices,MatrixList-method	matrices
MatrixList	MatrixList
MatrixList-class	MatrixList
mcols	reexports
mcols<-	reexports
modeq	modeq
mut_type	mut_type
names	AutomorphismList
names,AutomorphismList-method	AutomorphismList
names<-,AutomorphismList-method	AutomorphismList
readDNAMultipleAlignment	reexports
reexports	reexports
seqRanges	CodonSeq
seqranges	seqranges
seqRanges,CodonSeq-method	CodonSeq
seqranges,CodonSeq-method	seqranges
seqranges,DNAStringSet_OR_NULL-method	seqranges
setValidity2	reexports
show,AutomorphismList-method	AutomorphismList
show,CodonSeq-method	CodonSeq
show,MatrixList-method	MatrixList
show-AutomorphismList	AutomorphismList
show-CodonSeq	CodonSeq
show-MatrixList	MatrixList
slapply	slapply
sortByChromAndEnd	sortByChromAndStart
sortByChromAndStart	sortByChromAndStart
start	reexports
start<-	reexports
str2chr	str2chr
str2chr,character-method	str2chr
str2chr,list-method	str2chr
str2dig	str2dig
str2dig,character-method	str2dig
str2dig,list-method	str2dig
strand	reexports
strand<-	reexports
translate	reexports
translation	translation
translation,BioString-method	translation
translation,character-method	translation
valid.Automorphism	valid.Automorphism
valid.Automorphism.mcols	valid.Automorphism
valid.AutomorphismByCoef	valid.AutomorphismByCoef
valid.AutomorphismByCoefList	valid.AutomorphismByCoefList
valid.AutomorphismList	valid.AutomorphismList
valid.BaseGroup	valid.BaseGroup
valid.BaseGroup.elem	valid.BaseGroup
valid.CodonGroup	valid.CodonGroup
valid.CodonGroup.mcols	valid.CodonGroup
valid.ConservedRegion	ConservedRegion
valid.ConservedRegionList	ConservedRegion
valid.GRanges	valid.BaseGroup
valid.MatrixList	valid.MatrixList
width	reexports
[	extract-methods
[,AutomorphismList,ANY-method	extract-methods
[[	extract-methods
[[,AutomorphismList-method	extract-methods
