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.
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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.
library(MSA2dist)
# Load example data
data(hiv, package="MSA2dist")
# 1. Calculate pairwise DNA distances (K80 model)
dna_dist <- dnastring2dist(hiv, model="K80")
# 2. Translate to Amino Acids and calculate Grantham distances
aa_seqs <- cds2aa(hiv)
aa_dist <- aastring2dist(aa_seqs, score=granthamMatrix())
# 3. Calculate synonymous/nonsynonymous substitutions (MYN model)
kaks_myn <- dnastring2kaks(hiv, model="MYN")
Note: Input is a pre-aligned DNAStringSet object, and outputs are distance matrices and a data frame of Ka/Ks values.
Biostrings::AAStringSet using custom scoring matrices like Grantham's distance (aastring2dist, granthamMatrix).Biostrings::DNAStringSet using evolutionary models (e.g., "K80") or literal IUPAC distances for diploid phasing (dnastring2dist).dnastring2kaks).ape::dist.dna instead).mafft, muscle, or the R package msa first).Biostrings::DNAStringSet or Biostrings::AAStringSet.cds2aa(shorten=TRUE).dnastring2dist (e.g., "K80", "IUPAC") or dnastring2kaks (e.g., "Li", "NG86", "MYN", "YN").aastring2dist (e.g., granthamMatrix()).cds2aa.cds2aa.Biostrings::getGeneticCode("2")) in cds2aa.dnastring2dist or dnastring2kaks.cds2aa(shorten=TRUE) to handle sequences whose lengths are not multiples of three before translating.dnastring2dist(model="IUPAC") to directly calculate distances on IUPAC nucleotide ambiguity encoded sequences (e.g., from diploid individuals).shorten=FALSE. Fix: Set shorten=TRUE in cds2aa().DNAStringSet directly to ape or seqinr. Fix: Convert formats using dnastring2dnabin() or dnastring2aln().ape::dist.dna) and neighbor-joining trees.还没有评价。欢迎分享你的使用感受。
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