I have lots of ~250bp sequences & need to do local alignment. Tried EMBOSS water & matcher - they are good, but give just the best score. And I need something similar to BLAST2 where all the possible alignments are given. Hope someone could help me.
If water which performs full smith-waterman is efficient enough to map your number of sequences try ssearch which does exactly this. It comes with the fasta tools, has SSE support and multiple thread support such that it could be even faster. It will give you all there is to find (up to an evalue of 10 by default) which will also let you see a lot of bad alignments.
lalign36 does exactly what you want. It will show you all the non-overlapping alignments of a pair of sequences.
ssearch36 does something slightly different (and perhaps more like blast2seq); it will show you all of the parts of the target sequence that align with the query, but once part of the target is aligned, it will not be aligned again.
For example, in the sequence X A A B B Y vs Z A B A B V, both lalign36 and ssearch36 should show:
x a A B b y (here capital letters indicate actual alignment, z A B a b v lower case indicate context and are not aligned) x a A B b y z a b A B v
But lalign36 would also show:
x A a b b y z A b a b v x a a b B y z a b a B v x a a b B y z a B a b v x A a b b y z a b A b v