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<name>Clustal-Omega</name>
<version>1.1.0</version>
<doc>
<title>Clustal-omega</title>
<description>
<text lang="en">CLUSTAL-OMEGA is a general purpose multiple sequence alignment program.</text>
</description>
<authors>Fabian Sievers, Andreas Wilm, David Dineen and Des Higgins</authors>
<sourcelink>http://www.clustal.org/#Download</sourcelink>
<homepagelink>http://www.clustal.org</homepagelink>
<comment>
<text lang="en">Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable time.</text>
<text lang="en">In default mode, users give a file of sequences to be aligned and
these are clustered to produce a guide tree and this is used to guide
a "progressive alignment" of the sequences. There are also facilities
for aligning existing alignments to each other, aligning a sequence to
an alignment and for using a hidden Markov model (HMM) to help guide
an alignment of new sequences that are homologous to the sequences
used to make the HMM. This latter procedure is referred to as
"external profile alignment" or EPA.</text>
<text lang="en">Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
package from Johannes Soeding [1]. Guide trees are made using an
enhanced version of mBed [2] which can cluster very large numbers of
sequences in O(N*log(N)) time. Multiple alignment then proceeds by
aligning larger and larger alignments using HHalign, following the
clustering given by the guide tree.</text>
<text lang="en">In its current form Clustal-Omega can only align protein sequences but
not DNA/RNA sequences. DNA/RNA support has been added since version 1.1.0.</text>
</comment>
<reference doi="10.1038/msb.2011.75">Molecular Systems Biology 7 Article number: 539
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
</reference>
<reference doi="10.1093/bioinformatics/bti125">[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
comparison. Bioinformatics 21 (7): 951–960.</reference>
<reference doi="10.1186/1748-7188-5-21">[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence
embedding for fast construction of guide trees for multiple
sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.</reference>
</doc>
</package>
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