MUSCLE
MUSCLE is a program for creating multiple alignments of
amino acid or nucleotide sequences.
MUSCLE stands for MUltiple Sequence
Comparison by Log-
Expectation. MUSCLE is claimed to achieve
both better average accuracy and better speed than ClustalW2 or
T-Coffee,
depending on the chosen options.
In the
authors' tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there
Features include:
- Three different protein profile scoring functions are
supported:
- log-expectation score
- sum of pairs
score using either the PAM200 matrix
- VTML240 matrix
- Diagonal optimization
- Anchor optimization
- MUSCLE uses FASTA format for both input and output formats
- For output only, it also offers CLUSTALW, MSF, HTML, Phylip
sequential and Phylip
interleaved formats
Return
to Biology Tools Home Page
Last Updated Saturday, April 13 2013 @ 04:13 PM EDT
| 
