Version

Muscle v3.7 is available in Hippu
Muscle v3.6 is available in Muska

Description

Muscle is a fast and accurate sequence alignment program. It's novelty lies in the algorithm that initially creates a fast and crude alignment that is subsequently refined to a more optimal alignment.

Usage

In Hippu and Murska a basic alignment from FastA-formatted input sequences (here, in file inseqs.fasta) is created by the call:

muscle -in inseqs.fasta -out outseqs.fasta

Note that the output is also in FastA format. If you need to get the alignment in, say, Phylip format, you first need to save the alignment in muscle in Clustal-format. Then you need to open and save this alignment in Clustal in Phylip format. Clustal-formatted alignments can be produced with the following command:

muscle -in inseqs.fasta -out outseqs.fasta -clw -clwstrict

Options related to refining and creation of large alignment are described in detail in the manual.

Help

More detailed information about the program is available in the manual.

Reference

Please site: Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792-97.

Distribution

You can download Muscle (UNIX, Linux, Windows) from it's website.