alignFasta

Perform a Multiple Sequence Alignment on a FASTA file.

Perform a Multiple Sequence Alignment on a FASTA file.

Usage

alignFasta(fasta_file, tool = "Muscle", outpath = NULL)

alignFasta(fasta_file, tool = "Muscle", outpath = NULL)

Arguments

fasta_file

Path to the FASTA file to be aligned

tool

Type of alignment tool to use. One of three options: "Muscle", "ClustalO", or "ClustalW"

outpath

Path to write the resulting alignment to as a FASTA file. If NULL, no file is written

Value

aligned fasta sequence as a MsaAAMultipleAlignment object

aligned fasta sequence as a MsaAAMultipleAlignment object

Author

Samuel Chen, Janani Ravi

Examples

if (FALSE) { # \dontrun{
aligned_sequences <- alignFasta("my_sequences.fasta",
tool = "Muscle", outpath = "aligned_output.fasta")
} # }
if (FALSE) { # \dontrun{
# Example usage
aligned_sequences <- alignFasta("path/to/sequences.fasta",
tool = "ClustalO", outpath = "path/to/aligned_sequences.fasta")
aligned_sequences
} # }