[Biopython] How to optimize ACE file alignment (from newbler)

[Martin Mokrejs]

Hi,
  I would like to ask you how can I optimize the ACE alignment with files
produced by newbler. I see only the high-quality region is aligned while
the rest is not. I typically ask newbler to place into the ace files untrimmed
reads so the low-quality sequence is present, you can see it could have been
included in the alignment and contribute the consensus quite well.
  I found a new feature of consed-20 being able to re-align the reads 
but that seemed to be too slow for me and had to kill re-processing of one
contig.
  Is there a way to direct some program that I want to re-align just some
columns since some position? That should first align to the consensus already
defined and afterwards continue with de novo alignment as long as it is possible.
  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
move columns back and forth, re-order rows) and do you re-calculate the
consensus?
  This is some sort of a follow-up to "Newbler ACE file to SAM?"
posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
;)
Martin