Biology Reference
In-Depth Information
the command-line prompt, different operating systems and/or
shells may have different command-line prompts, like “
>
” or “%”):
$ tar -xvf Clustal-Omega-1.0.3
$ cd Clustal-Omega-1.0.3
$ ./configure
$ make
$ make install
This should configure, build, and install the Clustal Omega
package (
see Notes 2
-
4
). The last step may require root/sudo
privileges. However, make will still compile a Clustal Omega exe-
cutable, which can be moved to any location in the user's file tree
and can then be invoked by specifying the full path-name, for
example:
/home/clustal-user/path/to/where/clustal/is/located/clustalo
3 Methods
For now, Clustal Omega can only be run from the command-line.
To obtain a brief list of all available Clustal Omega command-line
flags type:
$ clustalo -h
and hit
<
return
>
.
Parts of the Clustal Omega code have beenmulti-threaded, using
OpenMP. By default, Clustal Omega will attempt to use all available
threads. To limit the number of threads one can specify --threads.
Despite Clustal Omega being very fast for many purposes,
some alignments may take a long time. In this case it may be
reassuring to track the real-time progress of the alignment. This
can be done by specifying the -v flag. This will print to screen what
phase the calculation is in (distance matrix calculation, k-means
clustering, guide-tree construction, progressive alignment).
Repeating the -v flag a second time increases the level of verbosity,
giving a more detailed progress report. Triple -v is the highest level
of verbosity, giving details about distances, tree building and inter-
mediate alignments. This level is only useful for the smallest align-
ments.
The most basic use of Clustal Omega involves aligning a number of
unaligned sequences that are all contained in a single file. For
example, if the file globin.fa contains more than two unaligned
sequences in fasta format, then:
3.1 Basic Multiple
Sequence Alignment
$ clustalo -i globin.fa
will read in the file, align the sequences and output the
alignment to screen (default) in the default (fasta) format.
