Which multiple alignment algorithm should I use?

Four different multiple alignment algorithms are available in Geneious Prime 2020 under Align/Assemble→Multiple Align. It is important to consider the size of your dataset when choosing which one to use.  Below is a brief overview of each algorithm. 

Geneious aligner

The Geneious aligner is a progressive pairwise aligner, similar to ClustalW (below).  It is the slowest algorithm in Geneious and recommended for small alignments (e.g. fewer than 50 sequences, less than 1 kb in length).


MUSCLE is a good choice for medium-large alignments of up to a few thousand taxa.   The algorithm is described at http://nar.oxfordjournals.org/content/32/5/1792.full.pdf+html and a full manual is available at http://www.drive5.com/muscle/manual/index.html.  The defaults are optimized for best accuracy.  However, you can reduce the run-time on large alignments without too much reduction in accuracy by reducing the maximum number of iterations.  

Clustal Omega (replaces ClustalW in Geneious Prime 2020 onwards)

Clustal Omega is a fast, accurate aligner suitable for alignments of any size.  It is multithreaded for faster alignment. A full description of the algorithms used by Clustal Omega is available in the Molecular Systems Biology paper Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Latest additions to Clustal Omega are described in Clustal Omega for making accurate alignments of many protein sciences.  See also the Clustal Omega website for further details.  

MAFFT (available as a plugin)

The MAFFT aligner is a good choice for large alignments (e.g. up to 30,000 sequences, or fewer long sequences).  Full details are given at http://mafft.cbrc.jp/alignment/software/. MAFFT plugin version 1.4 or later (available for R10 and later) supports multithreading for faster alignment.

For long sequences, the algorithm performs best if sequences are closely related.  For highly divergent sequences, a whole genome aligner like Mauve or LASTZ may be more efficient.  The MAFFT plugin can be installed by going to Tools→Plugins. 

ClustalW (available in Geneious Prime 2019 and earlier)

ClustalW is a progressive aligner similar to the Geneious aligner.  For details of the algorithm, see http://www-bimas.cit.nih.gov/clustalw/clustalw.html.  ClustalW is a little faster than Geneious, but should still be restricted to small alignments.


Have more questions? Submit a request