MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

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Documentation for package ‘MSA2dist’ version 1.10.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

aa2selfscore	aa2selfscore
aabin2aastring	aabin2aastring
AAMatrix	AAMatrix-data
AAMatrix-data	AAMatrix-data
aastring2aabin	aastring2aabin
aastring2aln	aastring2aln
aastring2dist	aastring2dist
addmask2string	addmask2string
addpop2string	addpop2string
addpos2string	addpos2string
addregion2string	addregion2string
aln2aastring	aln2aastring
aln2dnastring	aln2dnastring
cds2aa	cds2aa
cds2codonaln	cds2codonaln
cdsstring2codonaln	cdsstring2codonaln
codon2number	GENETIC_CODE_TCAG
codon2numberAMBIG	codon2numberAMBIG
codon2numberTCAG	codon2numberTCAG
codonmat2pnps	codonmat2pnps
codonmat2xy	codonmat2xy
compareCodons	compareCodons
dnabin2dnastring	dnabin2dnastring
dnastring2aln	dnastring2aln
dnastring2codonmat	dnastring2codonmat
dnastring2dist	dnastring2dist
dnastring2dnabin	dnastring2dnabin
dnastring2kaks	dnastring2kaks
GENETIC_CODE_TCAG	GENETIC_CODE_TCAG
getmask	getmask
getpos	getpos
globalDeletion	globalDeletion
granthamMatrix	granthamMatrix
hiv	hiv-data
hiv-data	hiv-data
indices2kaks	indices2kaks
iupac	iupac-data
iupac-data	iupac-data
iupacMatrix	iupacMatrix
makePostalignedSeqs	makePostalignedSeqs
pal2nal	pal2nal
popinteger	popinteger
popnames	popnames
rcpp_distSTRING	rcpp_distSTRING
rcpp_KaKs	rcpp_KaKs
rcpp_pairwiseDeletionAA	rcpp_pairwiseDeletionAA
rcpp_pairwiseDeletionDNA	rcpp_pairwiseDeletionDNA
region	region
regionused	regionused
string2region	string2region
subString	subString
uptriidx	uptriidx