aln2aastring: aln2aastring

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

aln2aastring

Description

This function converts a seqinr alignment into an AAStringSet.

Usage

aln2aastring(aln)

Arguments

aln	seqinr alignment [mandatory]

Value

An object of class AAStringSet

Author(s)

Kristian K Ullrich

See Also

as.alignment AAStringSet

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
#aastring2aln(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> aastring2aln() |> aln2aastring()

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.