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Perform a Multiple Sequence Alignment on a FASTA file.

Source: R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
alignFasta.Rd

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