MUSCLE
MUSCLE is a computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function -- "the log-expectation score" -- and refinement using tree-dependent restricted partitioning.
See: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 2004, Vol. 32, No. 5 1792-1797. Oxford University Press access.
FASTA format
FASTA format is described here.Typically, a FASTA format sequence consists of a line beginning with a ">" that provides the sequence name or description, followed by one or more lines with one-letter amino acid ("residue") codes.
Alignments on this server are limited to no more than 200 sequences.
If the alignment has more than 100 sequences, the number of iterations
that MUSCLE performs will be limited to 2.
MUSCLE is available for download, which will allow you
to run MUSCLE (without restriction) on your computer.
Upload FASTA file
Alternatively, sequences in a file on your local computer may be used
as the input seed.
The sequence file must be in
FASTA format.
Send email to
Email will be sent to this address announcing completion of the
MUSCLE run. The email will provide a URL link to the results.