MUSCLE
Encyclopedia
MUSCLE is public domain
, multiple sequence alignment
software for protein
and nucleotide
sequences.
MUSCLE is often used as a replacement for Clustal
, since it typically (but not always) gives better sequence alignments; in addition, MUSCLE is significantly faster than Clustal
, especially for larger alignments (Edgar 2004).
MUSCLE is integrated into UGENE
bioinformatics tool as a plugin.
Public domain
Works are in the public domain if the intellectual property rights have expired, if the intellectual property rights are forfeited, or if they are not covered by intellectual property rights at all...
, multiple sequence alignment
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
software for protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
and nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
sequences.
MUSCLE is often used as a replacement for Clustal
Clustal
Clustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
, since it typically (but not always) gives better sequence alignments; in addition, MUSCLE is significantly faster than Clustal
Clustal
Clustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
, especially for larger alignments (Edgar 2004).
MUSCLE is integrated into UGENE
UGENE
UGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...
bioinformatics tool as a plugin.
See also
- Sequence alignment softwareSequence alignment softwareThis list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment...
- ClustalClustalClustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
- ProbConsProbConsProbCons is an open source probabilistic consistency-based multiple alignment of amino acid sequences. It is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.- See also :*...
- AMAPAMAPAMAP is a multiple sequence alignment program based on a new approach to multiple alignment called sequence annealing. This approach consists of building up the multiple alignment one match at a time, thereby circumventing many of the problems of progressive alignment...
- T-COFFEET-CoffeeT-Coffee is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment...
- MAFFTMAFFTMAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. MAFFT is freely available for academic use, without any warranty.- External links :* * * at EBI* at GenomeNet* in MyHits, SIB...
- Geneious ProGeneiousGeneious is suite of cross-platform bioinformatics software applications developed by Biomatters Ltd.- Features :Geneious comes in a Basic version that is free for academic use, and a commercial Pro version with added features. Geneious bundles various bioinformatics tools under one hood with an...
includes MUSCLE as part of its all-in-one sequence analysis platform.