localalign and swalign

hi what is the difference between swalign and localalign?

both are local align . if the swalign is using smith-waterman alg., then what is localalign using? is using heuristic alg. such as blast?

many thanks

[Hadas Zur]

I would also be interested in the answer to this question

[Pete]

I'm not a bioinformatician, but use SW to align read & ref strings for testing. I'm presently doing longer reads (10kb+) and just tried the local align on these long reads, so for 11kb, swalign came back at 0.88sec and localalign with 5.75sec, so guess SW is just more efficient. For short reads, I'm guessing there'd be little difference, but it'd be interesting to hear view from someone who uses it!

Viewing the code, there are obviously differences - try the following:

edit swalign.m
edit localalign.m

Anyone else wanting to comment?