[EMBOSS] matcher output

[Karin Lagesen]

Hi!

I am trying to use matcher to align some sequences. I would however
like to get the whole sequences outputted. I think that this is what
the option -aglobal3 is for. I have tried 

matcher teste testb -outfile test.matcher -aglobal3 1

in various formats, including with = signs, with and without outfile
and with True instead of 1 too, but I cannot see any difference. I am
trying this with sequences where I should see a difference.

Does -aglobal3 do what I think it does, or isn't there an option to
matcher that does what I want it to do? In that case, is there a
different program out there which does what I need (i.e. a local
alignment of two sequences where the rest of the sequences are matched
together too).

TIA,

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at labmed.uio.no