aastring2aabin: aastring2aabin

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

aastring2aabin

Description

This function converts an AAStringSet into an ape AAbin.

Usage

aastring2aabin(aa)

Arguments

aa	AAStringSet [mandatory]

Value

An object of class AAbin

Author(s)

Kristian K Ullrich

See Also

as.alignment as.DNAbin.alignment

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
## convert into AAbin
#aastring2aabin(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> aastring2aabin()

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