GenomAutomorphism-package	GenomAutomorphism
$	extract-methods
$,AutomorphismList-method	extract-methods
$,ListCodonMatrix-method	extract-methods
$,MatrixSeq-method	extract-methods
'%%'	mod
'names<-'	AutomorphismList
'['	extract-methods
'[['	extract-methods
aaindex1	aaindex1
aaindex2	aaindex2
aaindex3	aaindex3
AAMultipleAlignment	reexports
AAStringSet	reexports
aa_index	aa_phychem_index
aa_mutmat	aa_phychem_index
aa_phychem_index	aa_phychem_index
aln	aln
aminoacid_dist	aminoacid_dist
aminoacid_dist,AAStringSet,ANY-method	aminoacid_dist
aminoacid_dist,character,character-method	aminoacid_dist
aminoacid_dist,CodonGroup_OR_Automorphisms,ANY-method	aminoacid_dist
aminoacid_dist,DNAStringSet,ANY-method	aminoacid_dist
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
automorphisms	automorphisms
automorphisms,DNAStringSet_OR_NULL-method	automorphisms
automorphism_bycoef	automorphism_bycoef
automorphism_bycoef,Automorphism-method	automorphism_bycoef
automorphism_bycoef,AutomorphismList-method	automorphism_bycoef
automorphism_prob	automorphism_prob
automorphism_prob,AutomorphismByCoef-method	automorphism_prob
automorphism_prob,AutomorphismByCoefList-method	automorphism_prob
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
BaseSeq	BaseSeq
BaseSeq-class	BaseSeq
BaseSeqMatrix	BaseSeqMatrix
BaseSeqMatrix-class	BaseSeqMatrix
base_coord	base_methods
base_coord,DNAStringSet_OR_NULL-method	base_methods
base_matrix	base_methods
base_matrix,DNAStringSet_OR_NULL-method	base_methods
base_methods	base_methods
base_repl	base_repl
base_seq2string_set	base_methods
base_seq2string_set,BaseSeq-method	base_methods
brca1_aln	brca1_aln
brca1_aln2	brca1_aln2
brca1_autm	brca1_autm
brca1_autm2	brca1_autm2
cdm_z64	cdm_z64
CodonGroup	CodonGroup
CodonGroup-class	CodonGroup
CodonMatrix	CodonMatrix
CodonMatrix-class	CodonMatrix
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
codon_dist	codon_dist
codon_dist,character-method	codon_dist
codon_dist,CodonGroup_OR_Automorphisms-method	codon_dist
codon_dist,DNAStringSet-method	codon_dist
codon_dist_matrix	codon_dist_matrix
codon_matrix	codon_matrix
codon_matrix,BaseSeqMatrix-method	codon_matrix
codon_matrix,DNAMultipleAlignment-method	codon_matrix
codon_matrix,DNAStringSet-method	codon_matrix
colMeans2	reexports
colSds	reexports
colSums2	reexports
colVars	reexports
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
DNAMultipleAlignment	reexports
DNAStringSet	reexports
DNAStringSet_OR_DNAMultipleAlignment-class	GRangesMatrixSeq
DNAStringSet_OR_NULL-class	valid.MatrixList
dna_phyche	dna_phyche
dna_phychem	dna_phychem
dna_phychem,character-method	dna_phychem
dna_phychem,DNAStringSet_OR_DNAMultipleAlignment-method	dna_phychem
end	reexports
end<-	reexports
extract	extract-methods
extract-methods	extract-methods
GENETIC_CODE_TABLE	reexports
GenomAutomorphism	GenomAutomorphism
getAutomorphisms	getAutomorphisms
getAutomorphisms,AutomorphismList-method	getAutomorphisms
getAutomorphisms,DataFrame_OR_data.frame-method	getAutomorphisms
getAutomorphisms,list-method	getAutomorphisms
getGeneticCode	reexports
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,BaseSeq,missing-method	get_mutscore
get_mutscore,character,character-method	get_mutscore
get_mutscore,DNAMultipleAlignment,missing-method	get_mutscore
get_mutscore,DNAStringSet,missing-method	get_mutscore
GRangesList	reexports
GRangesMatrixSeq	GRangesMatrixSeq
GRangesMatrixSeq-class	GRangesMatrixSeq
GRanges_OR_NULL-class	GRanges_OR_NULL
is.url	is.url
ListCodonMatrix	ListCodonMatrix
ListCodonMatrix-class	ListCodonMatrix
makeGRangesFromDataFrame	reexports
matrices	matrices
matrices,CodonSeq-method	matrices
matrices,DNAStringSet_OR_NULL-method	matrices
matrices,MatrixList-method	matrices
MatrixList	MatrixList
MatrixList-class	MatrixList
MatrixSeq	MatrixSeq
MatrixSeq-class	MatrixSeq
mcols	reexports
mcols<-	reexports
mod	mod
mod,matrix,numeric-method	mod
modeq	modeq
modlin	reexports
modlineq	modlineq
modq	reexports
modulo	mod
mut_type	mut_type
names,AutomorphismList-method	AutomorphismList
names,ListCodonMatrix-method	extract-methods
names<-,AutomorphismList-method	AutomorphismList
names<-,MatrixSeq-method	extract-methods
peptide_phychem_index	peptide_phychem_index
peptide_phychem_index,character-method	peptide_phychem_index
peptide_phychem_index,DNAStringSet_OR_DNAMultipleAlignment-method	peptide_phychem_index
readDNAMultipleAlignment	reexports
reexports	reexports
rowMeans2	reexports
rowSds	reexports
rowSums2	reexports
rowVars	reexports
seq2granges	base_methods
seq2granges,DNAStringSet_OR_NULL-method	base_methods
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	show-methods
show,ListCodonMatrix-method	show-methods
show,MatrixList-method	show-methods
show,MatrixSeq-method	MatrixSeq
show-AutomorphismList	AutomorphismList
show-CodonSeq	show-methods
show-ListCodonMatrix	show-methods
show-MatrixList	show-methods
show-MatrixSeq	MatrixSeq
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
subseq	reexports
translate	reexports
translation	translation
translation,BioString-method	translation
translation,character-method	translation
unmasked	reexports
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.ListCodonMatrix	ListCodonMatrix
valid.MatrixList	valid.MatrixList
width	reexports
[,AutomorphismList,ANY-method	extract-methods
[,ListCodonMatrix,ANY-method	extract-methods
[,MatrixSeq,ANY-method	extract-methods
[[,AutomorphismList-method	extract-methods
[[,ListCodonMatrix-method	extract-methods
