A brief introduction to CLUSTALW
CLUSTALW is a progressive multiple sequence alignment program. It proceeds in three steps. In the first one, all sequences are aligned by pair. Then, in the second, a dendogram is constructed describing the approximate groupings of the sequences by similarity. In the third, and last, the multiple alignment is built using the dendogram as a guide. It takes into account sequence weighting, positions-specific gap penalties and different weight matrix.
For further details, see CLUSTALW documentation.

Availability in NPS@
CLUSTALW is available :

The database to align cannot have more than 250,000 characters.
So, for example, you can use CLUSTALW to align a database of similar sequences built from a BLAST search or a PATTINPROT search.

Five output formats are available in CLUSTALW. Only clustalw format gives the output as described below. With other formats, the file is written to the page.
With the output order parameter you can choose to show the aligned sequences in the input order or in the aligned order (the dendogram order).
You have to choose between fast or slow pairwise alignment. For fast pairwise alignement, you can set the K-tuple (decrease for sensitivity), the number of tops diagonals (decrease for speed, increase for sensitivity), the window size (decrease for speed, increase for sensitivity), the gap penalty and the scoring method. For slow pairwise alignement, you can set the protein/DNA weight matrix, the gap opening penalty and the gap extension penalty.
The you can set the multiple alignment parameters : the protein/DNA weight matrix, the gap opening penalty, the gap extension penalty, the percent of identity for delay, the gap separation distance and the no end gap separation penalty. In case of proteins, other parameters are available : the residue-specific gap penalties, the hydrophilic residues and the hydrophilic gaps.

Pairwise alignment parameters control the speed and the sensitivity of the initial alignements.
Multiple alignment parameters control the gaps in the final multiple alignments.

NPS@ CLUSTALW output example
The NPS@ CLUSTALW output is divided into three parts.