Files in kullrich/MSA2dist

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

.Rbuildignore

.gitignore

CODE_OF_CONDUCT.md

DESCRIPTION

LICENSE

MSA2dist.Rproj

NAMESPACE

NEWS.md R/AAMatrix-data.R R/GENETIC_CODE_TCAG.R R/RcppExports.R R/aa2selfscore.R R/aabin2aastring.R R/aastring2aabin.R R/aastring2aln.R R/aastring2dist.R R/addmask2string.R R/addpop2string.R R/addpos2string.R R/addregion2string.R R/aln2aastring.R R/aln2dnastring.R R/cds2aa.R R/cds2codonaln.R R/cdsstring2codonaln.R R/codon2numberAMBIG.R R/codon2numberTCAG.R R/codonmat2pnps.R R/codonmat2xy.R R/compareCodons.R R/dnabin2dnastring.R R/dnastring2aln.R R/dnastring2codonmat.R R/dnastring2dist.R R/dnastring2dnabin.R R/dnastring2kaks.R R/getmask.R R/getpos.R R/globalDeletion.R R/granthamMatrix.R R/hiv-data.R R/indices2kaks.R R/iupac-data.R R/iupacMatrix.R R/makePostalignedSeqs.R R/pal2nal.R R/popinteger.R R/popnames.R R/region.R R/regionused.R R/string2region.R R/subString.R R/uptriidx.R README.md

data/AAMatrix.rda

data/hiv.rda

data/iupac.rda

man/AAMatrix-data.Rd man/GENETIC_CODE_TCAG.Rd man/aa2selfscore.Rd man/aabin2aastring.Rd man/aastring2aabin.Rd man/aastring2aln.Rd man/aastring2dist.Rd man/addmask2string.Rd man/addpop2string.Rd man/addpos2string.Rd man/addregion2string.Rd man/aln2aastring.Rd man/aln2dnastring.Rd man/cds2aa.Rd man/cds2codonaln.Rd man/cdsstring2codonaln.Rd man/codon2numberAMBIG.Rd man/codon2numberTCAG.Rd man/codonmat2pnps.Rd man/codonmat2xy.Rd man/compareCodons.Rd man/dnabin2dnastring.Rd man/dnastring2aln.Rd man/dnastring2codonmat.Rd man/dnastring2dist.Rd man/dnastring2dnabin.Rd man/dnastring2kaks.Rd

man/figures/logo.png

man/getmask.Rd man/getpos.Rd man/globalDeletion.Rd man/granthamMatrix.Rd man/hiv-data.Rd man/indices2kaks.Rd man/iupac-data.Rd man/iupacMatrix.Rd man/makePostalignedSeqs.Rd man/pal2nal.Rd man/popinteger.Rd man/popnames.Rd man/rcpp_KaKs.Rd man/rcpp_distSTRING.Rd man/rcpp_pairwiseDeletionAA.Rd man/rcpp_pairwiseDeletionDNA.Rd man/region.Rd man/regionused.Rd man/string2region.Rd man/subString.Rd man/uptriidx.Rd

src/GY94.cpp

src/GY94.h

src/KaKs.cpp

src/KaKs.h

src/LPB93.cpp

src/LPB93.h

src/LWL85.cpp

src/LWL85.h

src/MSMA.cpp

src/MSMA.h

src/MYN.cpp

src/MYN.h

src/NG86.cpp

src/NG86.h

src/RcppExports.cpp

src/YN00.cpp

src/YN00.h

src/base.cpp

src/base.h

src/rcpp_KaKs.cpp

src/rcpp_distSTRING.cpp

src/rcpp_pairwiseDeletionAA.cpp

src/rcpp_pairwiseDeletionDNA.cpp

tests/testthat.R tests/testthat/test-GENETIC_CODE_TCAG.R tests/testthat/test-aa2selfscore.R tests/testthat/test-aabin2aastring.R tests/testthat/test-aastring2aabin.R tests/testthat/test-aastring2aln.R tests/testthat/test-aastring2dist.R tests/testthat/test-addmask2string.R tests/testthat/test-addpop2string.R tests/testthat/test-addpos2string.R tests/testthat/test-addregion2string.R tests/testthat/test-aln2aastring.R tests/testthat/test-aln2dnastring.R tests/testthat/test-cds2aa.R tests/testthat/test-cds2codonaln.R tests/testthat/test-cdsstring2codonaln.R tests/testthat/test-codon2numberAMBIG.R tests/testthat/test-codon2numberTCAG.R tests/testthat/test-codonmat2pnps.R tests/testthat/test-codonmat2xy.R tests/testthat/test-compareCodons.R tests/testthat/test-dnabin2dnastring.R tests/testthat/test-dnastring2aln.R tests/testthat/test-dnastring2dist.R tests/testthat/test-dnastring2dnabin.R tests/testthat/test-dnastring2kaks.R tests/testthat/test-getmask.R tests/testthat/test-getpos.R tests/testthat/test-globalDeletion.R tests/testthat/test-granthamMatrix.R tests/testthat/test-indices2kaks.R tests/testthat/test-iupacMatrix.R tests/testthat/test-pal2nal.R tests/testthat/test-popinteger.R tests/testthat/test-popnames.R tests/testthat/test-rcpp_KaKs.R tests/testthat/test-rcpp_distSTRING.R tests/testthat/test-rcpp_pairwiseDeletionAA.R tests/testthat/test-rcpp_pairwiseDeletionDNA.R tests/testthat/test-region.R tests/testthat/test-string2region.R tests/testthat/test-subString.R tests/testthat/test-uptriidx.R vignettes/MSA2dist.Rmd

vignettes/bibliography.bib

kullrich/MSA2dist documentation built on April 26, 2024, 4:43 p.m.