Files in hyginn/shi
Multiple Sequence Alignment Handling and Inspection
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/balibaseTcScore.R
R/calcEntropy.R
R/calcHeights.R
R/calcInformation.R
R/calcMaxInformation.R
R/charUtils.R
R/clineshiftScore.R
R/compareColumn.R
R/data.R
R/generatePairMap.R
R/generateSettingsMap.R
R/getFrequencies.R
R/glyphPlot.R
R/glyphPoly.R
R/glyphUtils.R
R/isGap.R
R/loadCpp.R
R/makeGlyph.R
R/positionAlignment.R
R/readSequence.R
R/sequenceLogoR.R
R/shiWriteALN.R
R/simulationClosure.R
R/smallSampleCorrectionClosure.R
R/svgUtils.R
R/zzz.R
README.md
inst/extdata/aligned/aligned_MAFFT.fasta
inst/extdata/aligned/aligned_MUSCLE.fasta
inst/extdata/aligned/aligned_clustal-omega.fasta
inst/extdata/aligned/aligned_expresso.fasta
inst/extdata/aligned/aligned_kalign.fasta
inst/extdata/aligned/aligned_m-coffee.fasta
inst/extdata/aligned/aligned_psi-coffee.fasta
inst/extdata/aligned/aligned_t-coffee.fasta
inst/extdata/batik/CHANGES
inst/extdata/batik/LICENSE
inst/extdata/batik/NOTICE
inst/extdata/batik/README
inst/extdata/batik/batik-1.9.jar
inst/extdata/batik/batik-rasterizer-1.9.jar
inst/extdata/batik/batik-slideshow-1.9.jar
inst/extdata/batik/batik-squiggle-1.9.jar
inst/extdata/batik/batik-svgpp-1.9.jar
inst/extdata/batik/batik-ttf2svg-1.9.jar
inst/extdata/batik/extensions/README.txt
inst/extdata/batik/extensions/batik-rasterizer-ext-1.9.jar
inst/extdata/batik/extensions/batik-squiggle-ext-1.9.jar
inst/extdata/batik/lib/LICENSE.dom-documentation.txt
inst/extdata/batik/lib/LICENSE.dom-software.txt
inst/extdata/batik/lib/LICENSE.fop-transcoder-allinone-2.2.txt
inst/extdata/batik/lib/LICENSE.js.txt
inst/extdata/batik/lib/LICENSE.sax.txt
inst/extdata/batik/lib/LICENSE.xalan-2.7.0.txt
inst/extdata/batik/lib/LICENSE.xerces_2_5_0.txt
inst/extdata/batik/lib/LICENSE.xmlgraphics-commons-2.2.txt
inst/extdata/batik/lib/README.fop-transcoder-allinone-2.2.txt
inst/extdata/batik/lib/README.js.txt
inst/extdata/batik/lib/README.xalan-2.7.0.txt
inst/extdata/batik/lib/README.xerces_2_5_0.txt
inst/extdata/batik/lib/README.xml-apis-1.3.04.txt
inst/extdata/batik/lib/README.xml-apis-ext-1.3.04.txt
inst/extdata/batik/lib/Squiggle.icns
inst/extdata/batik/lib/batik-all-1.9.jar
inst/extdata/batik/lib/batik-anim-1.9.jar
inst/extdata/batik/lib/batik-awt-util-1.9.jar
inst/extdata/batik/lib/batik-bridge-1.9.jar
inst/extdata/batik/lib/batik-codec-1.9.jar
inst/extdata/batik/lib/batik-css-1.9.jar
inst/extdata/batik/lib/batik-dom-1.9.jar
inst/extdata/batik/lib/batik-ext-1.9.jar
inst/extdata/batik/lib/batik-extension-1.9.jar
inst/extdata/batik/lib/batik-gui-util-1.9.jar
inst/extdata/batik/lib/batik-gvt-1.9.jar
inst/extdata/batik/lib/batik-parser-1.9.jar
inst/extdata/batik/lib/batik-script-1.9.jar
inst/extdata/batik/lib/batik-svg-dom-1.9.jar
inst/extdata/batik/lib/batik-svggen-1.9.jar
inst/extdata/batik/lib/batik-swing-1.9.jar
inst/extdata/batik/lib/batik-transcoder-1.9.jar
inst/extdata/batik/lib/batik-util-1.9.jar
inst/extdata/batik/lib/batik-xml-1.9.jar
inst/extdata/batik/lib/fop-transcoder-allinone-2.2.jar
inst/extdata/batik/lib/js.jar
inst/extdata/batik/lib/serializer-2.7.2.jar
inst/extdata/batik/lib/xalan-2.7.2.jar
inst/extdata/batik/lib/xercesImpl-2.9.1.jar
inst/extdata/batik/lib/xml-apis-1.3.04.jar
inst/extdata/batik/lib/xml-apis-ext-1.3.04.jar
inst/extdata/batik/lib/xmlgraphics-commons-2.2.jar
inst/extdata/example.txt
inst/extdata/example2.txt
inst/extdata/example2ref.txt
inst/extdata/exampleref.txt
inst/extdata/noGapsRefAPSES.fasta
inst/extdata/notosans/DESCRIPTION.en_us.html
inst/extdata/notosans/NotoSans-Bold.ttf
inst/extdata/notosans/NotoSans-BoldItalic.ttf
inst/extdata/notosans/NotoSans-Italic.ttf
inst/extdata/notosans/NotoSans-Regular.ttf
inst/extdata/notosans/OFL.txt
inst/extdata/refAPSES.mfa
inst/extdata/sawarbi/DESCRIPTION.en_us.html
inst/extdata/sawarbi/OFL.txt
inst/extdata/sawarbi/SawarabiMincho-Regular.ttf
inst/scripts/Logos2.1.pl
inst/scripts/UTF2glyph.R
inst/scripts/clineShiftScoreExamples.R
inst/scripts/functionTemplate.R
inst/scripts/glyphTools.R
inst/scripts/rcppDemos.R
man/.gitignore
shi.Rproj
src/.gitignore
src/RcppExports.cpp
src/codonSplit1.cpp
src/codonSplit2.cpp
src/codonSplit3.cpp
src/hello.cpp
tests/testthat.R
tests/testthat/testDummy.R
tests/testthat/test_balibaseTcScore.R
tests/testthat/test_calcEntropy.R
tests/testthat/test_calcHeights.R
tests/testthat/test_calcInformation.R
tests/testthat/test_calcMaxInformation.R
tests/testthat/test_clineShiftScore.R
tests/testthat/test_generatePairMap.R
tests/testthat/test_getFrequencies.R
tests/testthat/test_isGap.R
tests/testthat/test_sequenceLogoR.R
tests/testthat/test_shiWriteALN.R
tests/testthat/test_simulationClosure.R
tests/testthat/test_smallSampleCorrectionClosure.R
vignettes/Extensive-Guide-To-Shi.Rmd
vignettes/refs.bib
