ClustalW- for Multiple Alignment

ClustalW is a general purpose multiple alignment program for DNA or proteins [4]. ClustalW improves the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. It can create multiple alignments, manipulate existing alignments, perform profile analysis and create phylogenetic trees. Alignment can be constructed either slow but accurate or by fast but more approximated.
The input file for clustalW is a file containing all sequences in one of the formats: NBRF/PIR, EMBL/SwissProt, Pearson (FastA), GDE, Clustal, GCG/MSF, RSF.
One of the variants of ClustalW is ClastalX [14]. This variant provides a new window-based user interface to the ClustalW program (see the next figure for an example) NCBI site: [26]

  

Figure 4.3: An example of alignment from ClustalX