aastring2aln: aastring2aln

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

aastring2aln

Description

This function converts a AAStringSet into an seqinr alignment.

Usage

aastring2aln(aa)

Arguments

aa	AAStringSet [mandatory]

Value

An object of class alignment which is a list with the following components:
nb the number of aligned sequences
nam a vector of strings containing the names of the aligned sequences
seq a vector of strings containing the aligned sequences
com a vector of strings containing the commentaries for each sequence or NA if there are no comments

Author(s)

Kristian K Ullrich

See Also

as.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))
#aastring2aln(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> aastring2aln()

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