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

## Documentation for package ‘MSA2dist’ version 1.10.0

- 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