Package: MSA2dist 1.17.1
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 calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies.
Authors:
MSA2dist_1.17.1.tar.gz
MSA2dist_1.17.1.zip(r-4.7)MSA2dist_1.17.1.zip(r-4.6)MSA2dist_1.17.1.zip(r-4.5)
MSA2dist_1.17.1.tgz(r-4.6-x86_64)MSA2dist_1.17.1.tgz(r-4.6-arm64)MSA2dist_1.17.1.tgz(r-4.5-x86_64)MSA2dist_1.17.1.tgz(r-4.5-arm64)
MSA2dist_1.17.1.tar.gz(r-4.7-arm64)MSA2dist_1.17.1.tar.gz(r-4.7-x86_64)MSA2dist_1.17.1.tar.gz(r-4.6-arm64)MSA2dist_1.17.1.tar.gz(r-4.6-x86_64)
MSA2dist_1.17.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSA2dist/json (API)
NEWS
| # Install 'MSA2dist' in R: |
| install.packages('MSA2dist', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Pkgdown/docs site:https://mpievolbio-it.pages.gwdg.de
On BioConductor:MSA2dist-1.17.0(bioc 3.24)MSA2dist-1.16.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
alignmentsequencinggeneticsgocpp
Last updated from:0336f4dc54. Checks:12 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 222 | ||
| linux-devel-arm64 | NOTE | 346 | ||
| linux-devel-x86_64 | NOTE | 386 | ||
| source / vignettes | OK | 360 | ||
| linux-release-arm64 | NOTE | 351 | ||
| linux-release-x86_64 | NOTE | 425 | ||
| macos-release-arm64 | NOTE | 173 | ||
| macos-release-x86_64 | NOTE | 536 | ||
| macos-oldrel-arm64 | NOTE | 289 | ||
| macos-oldrel-x86_64 | NOTE | 555 | ||
| windows-devel | NOTE | 477 | ||
| windows-release | NOTE | 515 | ||
| windows-oldrel | NOTE | 472 | ||
| wasm-release | OK | 147 |
Exports:aa2selfscoreaabin2aastringaastring2aabinaastring2alnaastring2distaddmask2stringaddpop2stringaddpos2stringaddregion2stringaln2aastringaln2dnastringcds2aacds2codonalncdsstring2codonalncodon2numberAMBIGcodon2numberTCAGcodonmat2pnpscodonmat2xycompareCodonsdnabin2dnastringdnastring2alndnastring2codonmatdnastring2distdnastring2dnabindnastring2kaksGENETIC_CODE_TCAGgetmaskgetposglobalDeletionglobalDeletionAAgranthamMatrixindices2kaksiupacMatrixmakePostalignedSeqspal2nalpopintegerpopnamesrcpp_distSTRINGrcpp_KaKsrcpp_pairwiseDeletionAArcpp_pairwiseDeletionDNAregionregionusedstring2regionsubStringuptriidx
Dependencies:ade4apeBiocGenericsBiostringsclicodetoolscpp11crayondigestdoParalleldplyrforeachgenericsGenomicRangesglueIRangesiteratorslatticelifecyclemagrittrMASSMultipleAlignmentnlmepillarpixmappkgconfigpurrrpwalignR6RcppRcppArmadilloRcppThreadrlangS4VectorssegmentedSeqinfoseqinrspstringistringrtibbletidyrtidyselectutf8vctrswithrXVector
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 |
