Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences - Multiple Sequence Alignment Methods - page 106

This will perform an initial alignment. It will then derive
new distances between sequences from this alignment and con-
struct a new guide-tree. It will also convert the initial alignment
into a HMM and use this HMM in a second round of
profile-profile alignment. After this second round the final align-
ment is written to the screen. Guide-tree iteration and HMM
iteration can be decoupled in the following way:
$ clustalo -i globin.fa --iter ¼ 5 --max-guidetree-

¼

iterations 1

This performs an initial alignment. In a second round
(first iteration) one reconstruction of the guide-tree is performed
in tandemwith one profile-profile alignment using a HMMderived
from the initial alignment. Four subsequent refinement rounds will
use HMMs derived from the previous alignments but will not
recalculate the guide-tree. Conversely, one can restrict the number
of HMM iterations, while repeatedly refining the guide-tree, by
setting --max-hmm-iterations to a value less than the one specified
by --iter. However, this variant is probably less useful as it does not
use any HMM information at the last alignment step ( see Note 7 ).

Profile Alignment When reading in aligned sequences, Clustal Omega makes use of
the alignment information (full alignment distances for guide-tree
construction and HMM information for EPA) and then “dealigns”
the sequences (removes all gaps) before realigning them. If the
--dealign flag is specified, then the sequences are dealigned without
making use of the alignment information. Sometimes this is not
desirable. For example, one might have a high-quality, hand-
curated alignment to which some unaligned sequences are to be
added, while keeping the curated alignment fixed. Alternatively,
one might want to align two profiles. In these cases one has to
use the Clustal Omega --profile flag. To align two profiles use
( see Note 8 ):

3.4

¼ ¼

$ clustalo --profile1 globin1.aln --profile2

globin2.aln
If more than one unaligned sequences are to be added to an
existing profile use:

¼

$ clustalo --profile1 globin1.aln -i moreGlobins.fa

Clustal Omega extracts HMM information from the profile
and uses this HMM as an external profile for EPA of the alignment
of the unaligned sequences. Once all the unaligned sequences have
been aligned this new profile is aligned to the previously existing
profile.