msa: Multiple Sequence Alignment

In orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants

Multiple Sequence Alignment

Description

Aligns multiple protein, DNA or CDS sequences using inhouse software.

Usage

msa(sequences, ids = names(sequences), seqtype = "prot", method, sfile = FALSE)

Arguments

sequences	vector containing the sequences as strings.
ids	character vector containing the sequences' ids.
seqtype	it should be either "prot" of "dna" or "cds" (see details).
method	the software to be used for the alignment, as invoked in your system. For instance, "muscle3" or "clustalo".
sfile	if different to FALSE, then it should be a string indicating the path to save a fasta alignment file.

Details

Either Clustal Omega or MUSCLE must be installed, and their executable be in your system's PATH. If seqtype is set to "cds" the sequences must not contain stop codons and they will be translated using the standard code. Afterward, the amino acid alignment will be used to lead the codon alignment.

Value

Returns a list of four elements. The first one ($seq) provides the sequences analyzed, the second element ($id) returns the identifiers, the third element ($aln) provides the alignment in fasta format and the fourth element ($ali) gives the alignment in matrix format.

Examples

## Not run: msa(sequences = c("APGW", "AGWC", "CWGA"),
                             ids = c("a", "b", "c"))
## End(Not run)

orthGS documentation built on June 8, 2025, 12:37 p.m.