ClustalW question - on multiple alignment of DNA sequences (Feb/24/2011 )

Hi all

I would like to generate a tree based on multiple DNA sequence alignment from ClustalW. I have not trimmed my sequences, but under the default ClustalW setting, does it only calculate the similarities on the region where all sequences are aligned? In another words, if I have some sequences that are longer than others, will these regions be calculated as gaps?

I have posted an image of my alignment for visual aid: will the gap seen in sequence 2/1-829 be seen as differing from the other 3 sequences?

http://i51.tinypic.com/258o39g.jpg

Thanks for any input.

I don't know the answer to the question directly, but you could find out by a little experiment....

You could trim one of the longer sequences to be the same size as the shorter sequence (say trim 1/1-892 to the A at 125), give it a new name, and include it (along with the full-length 1/1-892) in a mock alignment. See if ClustalW places the shortened 1/1-892 in a different place in the tree than the full-length 1/1-892...