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.
Version on CSC's Servers
In Taito MUSCLE is taken in use with command:
module load biokit
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 MUSCLE manual.
Information on setting up a batch job in Taito can be found in the Taito manual.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113.