[BiO BB] Constructing a multiple aligner, similar to Smith-Waterman

[Theodore H. Smith]

Hi people,

I am trying to figure out how to construct my own multiple aligner.  
Not because I expect it to be better than other aligners, but because  
I need to learn about alignment for a larger project. I need to get  
this all figured out.

I know that when aligning a Smith-Waterman based aligner, we start  
from the highest cell in the matrix, and trace backwards. But what if  
the trace actually has multiple highest cells? Or what if it goes  
like this:

13, 11, 13, 10, 9, 6, 3, 1, 0

That is, the trace has multiple highest cells within it, two 13's. Do  
we use the shorter back trace?

OK, so let's assume we got a single alignment done. How do we then  
find the other sections to align? Would a process of elimination do  
it? That is, search the remaining matrix (Excluding the portion  
already aligned) for the highest cell?

All this Smith-Waterman understanding I'm gaining is going into go  
into an experimental project I am working on, that I have no idea if  
it will be practical or not. I know it will work, I just don't know  
that it will give anyone any benefits over what they already got :)  
Needless to say, it's exciting stuff for people like me who like  
giving something new a go, I suppose the danger of it not being  
useful is half the excitement.