Provided by: clustalo_1.2.4-1_amd64 
NAME
clustalo - General purpose multiple sequence alignment program for proteins
SYNOPSIS
clustalo [-h]
DESCRIPTION
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.
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.
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.
In its current form Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is
envisioned that DNA/RNA will become available in a future version.
USAGE
Tool usage is available in /usr/share/doc/clustalo/README.
DEVELOPMENT
Headers and libraries are available in libclustalo-dev package.
CITING
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein
multiple sequence alignments
using Clustal Omega. Mol Syst Biol 7.
AUTHOR
Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo