Introduction | Installation | Load MSA2dist | Sequence Format conversion | Frame aware Biostrings::DNAStringSet translation (cds2aa()) | Pairwise sequence comparison | Calculate pairwise AA distances (aastring2dist()) | Grantham's distance | Calculate pairwise DNA distances (dnastring2dist()) | ape::dist.dna models | IUPAC distance | Coding sequences | Calculating synonymous and nonsynonymous substitutions (dnastring2kaks()) | Using any model from KaKs_Calculator 2.0 | Using indices to calculate Ka/Ks | Codon comparison | Create codon matrix (dnastring2codonmat()) | Calculate average behavior of each codon (codonmat2xy()) | Plot average behavior of each codon | Dxy and FST | Dxy and FST from pre-calculated distance matrix (dist2dxy()) | Dxy and FST directly from Biostrings::DNAStringSet (dnastring2dxy()) | References | Session Info
Package: MSA2dist 1.17.8
Kristian K Ullrich
MSA2dist: MSA2dist calculates pairwise distances for DNAStringSet/AAStringSet using custom scoring, conducts codon analyses (including dNdS), and estimates Dxy/FST
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. In addition, MSA2dist provides population genetic analyses, including the calculation of nucleotide divergence between populations (Dxy) and genetic differentiation statistics (FST) from aligned sequence data.
Authors:
MSA2dist_1.17.8.tar.gz
MSA2dist_1.17.8.zip(r-4.7)MSA2dist_1.17.8.zip(r-4.6)MSA2dist_1.17.8.zip(r-4.5)
MSA2dist_1.17.8.tgz(r-4.6-x86_64)MSA2dist_1.17.8.tgz(r-4.6-arm64)MSA2dist_1.17.8.tgz(r-4.5-x86_64)MSA2dist_1.17.8.tgz(r-4.5-arm64)
MSA2dist_1.17.8.tar.gz(r-4.7-arm64)MSA2dist_1.17.8.tar.gz(r-4.7-x86_64)MSA2dist_1.17.8.tar.gz(r-4.6-arm64)MSA2dist_1.17.8.tar.gz(r-4.6-x86_64)
MSA2dist_1.17.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MSA2dist/json (API)
| # Install 'MSA2dist' in R: |
| install.packages('MSA2dist', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kullrich/msa2dist/issues
On BioConductor:MSA2dist-1.17.6(bioc 3.24)MSA2dist-1.16.0(bioc 3.23)
alignmentsequencinggeneticsgobioconductor-packagebioinformaticsdndsdnds-estimationiupackaksmsa2distmultiple-sequence-alignmentscore-matrixcpp
Last updated from:bf677287ca. Checks:1 NOTE, 10 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 237 | ||
| linux-devel-arm64 | OK | 338 | ||
| linux-devel-x86_64 | OK | 389 | ||
| source / vignettes | OK | 327 | ||
| linux-release-arm64 | OK | 320 | ||
| linux-release-x86_64 | OK | 403 | ||
| macos-release-arm64 | OK | 197 | ||
| macos-release-x86_64 | OK | 775 | ||
| macos-oldrel-arm64 | ERROR | 265 | ||
| macos-oldrel-x86_64 | ERROR | 416 | ||
| windows-devel | OK | 475 | ||
| windows-release | OK | 494 | ||
| windows-oldrel | ERROR | 456 | ||
| wasm-release | OK | 182 |
Exports:aa2selfscoreaabin2aastringaastring2aabinaastring2alnaastring2distaddmask2stringaddpop2stringaddpos2stringaddregion2stringaln2aastringaln2dnastringcds2aacds2codonalncdsstring2codonalncodon2numberAMBIGcodon2numberTCAGcodonmat2pnpscodonmat2xycollapseCharcollapseXStringSetcompareCodonsdist2dxydnabin2dnastringdnastring2alndnastring2codonmatdnastring2distdnastring2dnabindnastring2dxydnastring2kaksdnastring2weightedPiGENETIC_CODE_TCAGgetmaskgetposglobalDeletionglobalDeletionAAgranthamMatrixindices2kaksiupacMatrixmakePostalignedSeqsnormpoppal2nalpopintegerpopnamesrcpp_distSTRINGrcpp_dxy_fst_poprcpp_KaKsrcpp_pairwiseDeletionAArcpp_pairwiseDeletionDNArcpp_weightedPircpp_weightedPi_popregionregionusedstring2regionsubStringuptriidx
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 |
| collapseChar | collapseChar |
| collapseXStringSet | collapseXStringSet |
| compareCodons | compareCodons |
| dist2dxy | dist2dxy |
| dnabin2dnastring | dnabin2dnastring |
| dnastring2aln | dnastring2aln |
| dnastring2codonmat | dnastring2codonmat |
| dnastring2dist | dnastring2dist |
| dnastring2dnabin | dnastring2dnabin |
| dnastring2dxy | dnastring2dxy |
| dnastring2kaks | dnastring2kaks |
| dnastring2weightedPi | dnastring2weightedPi |
| 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 |
| normpop | normpop |
| pal2nal | pal2nal |
| popinteger | popinteger |
| popnames | popnames |
| rcpp_distSTRING | rcpp_distSTRING |
| rcpp_dxy_fst_pop | rcpp_dxy_fst_pop |
| rcpp_KaKs | rcpp_KaKs |
| rcpp_pairwiseDeletionAA | rcpp_pairwiseDeletionAA |
| rcpp_pairwiseDeletionDNA | rcpp_pairwiseDeletionDNA |
| rcpp_weightedPi | rcpp_weightedPi |
| rcpp_weightedPi_pop | rcpp_weightedPi_pop |
| region | region |
| regionused | regionused |
| string2region | string2region |
| subString | subString |
| uptriidx | uptriidx |
