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  "Title": "MSA2dist calculates pairwise distances between all sequences of\na DNAStringSet or a AAStringSet using a custom score matrix and\nconducts codon based analysis",
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  "Description": "MSA2dist calculates pairwise distances between all\nsequences of a DNAStringSet or a AAStringSet using a custom\nscore matrix and conducts codon based analysis. It uses scoring\nmatrices to be used in these pairwise distance calculations\nwhich can be adapted to any scoring for DNA or AA characters.\nE.g. by using literal distances MSA2dist calculates pairwise\nIUPAC distances. DNAStringSet alignments can be analysed as\ncodon alignments to look for synonymous and nonsynonymous\nsubstitutions (dN/dS) in a parallelised fashion using a variety\nof substitution models. Non-aligned coding sequences can be\ndirectly used to construct pairwise codon alignments\n(global/local) and calculate dN/dS without any external\ndependencies.",
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      "title": "MSA2dist Vignette",
      "author": "Kristian K Ullrich",
      "engine": "knitr::rmarkdown",
      "headings": [
        "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",
        "References",
        "Session Info"
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      "created": "2021-12-22 23:24:09",
      "modified": "2025-03-28 08:07:37",
      "commits": 4
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