Package: MSA2dist 1.11.1
Kristian K Ullrich
MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.
Authors:
MSA2dist_1.11.1.tar.gz
MSA2dist_1.11.1.zip(r-4.5)MSA2dist_1.11.1.zip(r-4.4)
MSA2dist_1.11.1.tgz(r-4.4-x86_64)MSA2dist_1.11.1.tgz(r-4.4-arm64)
MSA2dist_1.11.1.tar.gz(r-4.5-noble)MSA2dist_1.11.1.tar.gz(r-4.4-noble)
MSA2dist_1.11.1.tgz(r-4.4-emscripten)
MSA2dist.pdf |MSA2dist.html✨
MSA2dist/json (API)
NEWS
| # Install 'MSA2dist' in R: |
| install.packages('MSA2dist', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Pkgdown site:https://mpievolbio-it.pages.gwdg.de
On BioConductor:MSA2dist-1.11.1(bioc 3.21)MSA2dist-1.10.1(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
alignmentsequencinggeneticsgocpp
Last updated 2 months agofrom:b5ab0385ca. Checks:1 OK, 5 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 17 2025 |
| R-4.5-win-x86_64 | NOTE | Jan 17 2025 |
| R-4.5-linux-x86_64 | NOTE | Jan 17 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 17 2025 |
| R-4.4-mac-x86_64 | NOTE | Jan 17 2025 |
| R-4.4-mac-aarch64 | NOTE | Jan 17 2025 |
Exports:aa2selfscoreaabin2aastringaastring2aabinaastring2alnaastring2distaddmask2stringaddpop2stringaddpos2stringaddregion2stringaln2aastringaln2dnastringcds2aacds2codonalncdsstring2codonalncodon2numberAMBIGcodon2numberTCAGcodonmat2pnpscodonmat2xycompareCodonsdnabin2dnastringdnastring2alndnastring2codonmatdnastring2distdnastring2dnabindnastring2kaksGENETIC_CODE_TCAGgetmaskgetposglobalDeletionglobalDeletionAAgranthamMatrixindices2kaksiupacMatrixmakePostalignedSeqspal2nalpopintegerpopnamesrcpp_distSTRINGrcpp_KaKsrcpp_pairwiseDeletionAArcpp_pairwiseDeletionDNAregionregionusedstring2regionsubStringuptriidx
Dependencies:ade4apeaskpassBiocGenericsBiostringsclicodetoolscpp11crayoncurldigestdoParalleldplyrfansiforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelatticelifecyclemagrittrMASSmimenlmeopensslpillarpixmappkgconfigpurrrpwalignR6RcppRcppArmadilloRcppThreadrlangS4VectorssegmentedseqinrspstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| aa2selfscore | aa2selfscore |
| aabin2aastring | aabin2aastring |
| AAMatrix-data | AAMatrix 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 |
| 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 | codon2number GENETIC_CODE_TCAG |
| getmask | getmask |
| getpos | getpos |
| globalDeletion | globalDeletion |
| globalDeletionAA | globalDeletionAA |
| granthamMatrix | granthamMatrix |
| hiv-data | hiv hiv-data |
| indices2kaks | indices2kaks |
| iupac-data | iupac 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 |
