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