msalign: Multiple alignment

In microseq: Basic Biological Sequence Handling

Multiple alignment

Description

Quickly computing a smallish multiple sequence alignment.

Usage

msalign(fsa.tbl, machine = "microseq::muscle")

Arguments

fsa.tbl	A fasta object (tibble) with input sequences.
machine	Function that does the 'dirty work'.

Details

This function computes a multiple sequence alignment given a set of sequences in a fasta object, see readFasta for more on fasta objects.

It is merely a wrapper for the function named in machine to avoid explicit writing and reading of files. This function should only be used for small data sets, since no result files are stored. For heavier jobs, use the machine function directly.

At present, the only machine function implemented is muscle, but other third-party machines may be included later.

Note that this function will run muscle with default settings, which is fine for small data sets.

Value

Results are returned as a fasta object, i.e. a tibble with columns ‘⁠Header⁠’ and ‘⁠Sequence⁠’.

Author(s)

Lars Snipen.

See Also

muscle, msaTrim.

Examples

## Not run: 
prot.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.faa")
faa <- readFasta(prot.file)
msa <- msalign(faa)

## End(Not run)

microseq documentation built on Aug. 21, 2023, 5:10 p.m.