Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. Clustal Omega improves on ClustalW mainly through increased alignment accuracy and improved scaling to many sequences.
- Clustal Omega doesn't perform pairwise alignment (you must input at least 3 sequences) and there is currently a limit of 4000 sequences or a maximum file size of 4MB of data.
- Clustal Omega can perform MSA's of proteins, DNA and RNA.
- Formatting can sometimes be an issue requiring to eliminate hidden characters or long headings
Website is straightforward and easy to use, with an extensive help page (see below).
- Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins D Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Molecular Systems Biology 7 Article number: 539 doi:10.1038/msb.2011.75
- A new bioinformatics analysis tools framework at EMBL-EBI (2010) Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R Nucleic acids research 2010 Jul, 38 Suppl: W695-9 doi:10.1093/nar/gkq313