From Wikipedia,
the free encyclopedia.
Clustal This is a widely
used multiple alignment program.
The latest version is 1.83. There
are two main variations:
ClustalW: command line
interface.
ClustalX: This is version have
graphical user interface. It is
availabe for Windows, Mac OS and
Unix/Linux
This program is available from
European Bioinformatics Institute
ftp server. Choose unix
for Unix/Linux, mac for Mac
OS, or dos for Windows
Input/Output
This program accept wide range
on input format. Included NBRF/PIR,
Fasta, EMBL/Swissprot, Clustal,
GCC/MSF, GCG9 RSF and GDE
The output format can be one or
many of the following: Clustal,
NBRF/PIR, GCG/MSF, PHYLIP, GDE,
NEXUS.
Multiple sequence alignment
There are 3 main steps:
- Do a pairwise alignment
- Create phylogenetic tree (or
use user define tree)
- Use the phylogenetic tree to
carry out a multiple alignment
These are done automatically
when you select "Do Complete
Alignment" Other options are "Do
Alignmetn from guide tree" and
"Produce guild tree only"
Profile alignments
Pairwise alignments are
computed for all against all
sequences, and similarities are
stored in a matrix. This is then
converted into a distance matrix,
where the distance measures
reflect the evolutionary distance
between each pair of sequences.
From this distance matrix, a
guide tree, or phylogenetic tree,
for the order in which pairs of
sequences are to be aligned and
combined with previous alignments
is constructed using a neighbour-joining
clustering algorithm. Sequences
are progessively aligned at each
branch point, starting from the
least distant pair of sequences.
Setting
User can align the sequences
with default setting. But
sometimes it's useful to customers
your own parameters.
The main parameters are the gap
opening penalty, gap extension
penalty
References
Thompson,J.D., Gibson,T.J.,
Plewniak,F., Jeanmougin,F. and
Higgins,D.G. (1997) The ClustalX
windows interface: flexible
strategies for multiple sequence
alignment aided by quality
analysis tools. Nucleic Acids
Research, 24:4876-4882.
