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clustalo - General purpose multiple sequence alignment program for proteins


clustalo [-h]


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.


Tool usage is available in /usr/share/doc/clustalo/README.


Headers and libraries are available in libclustalo-dev package.


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.

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