PileUp - how to align sequences > 7 kB

Mike Mitchell m.mitchell at icrf.icnet.uk
Tue Jun 23 03:57:35 EST 1998

In article <tbu-2206982003370001 at tburmei.dialup.fu-berlin.de>, tbu at gmx.net
(Thomas Burmeister) wrote:

> Dear Newsgroup-readers & GCG-users!
> I want to align sequences, appr. 10-15 kB in length. As I understand it,
> the GCG program PILEUP only supports alignments of sequences <= 7 kB. Is
> there a possibility to  circumvent this restriction? Or are there
> (freeware/shareware) multiple alignment programs, that can do this,
> available somewhere?

Pileup, as shipped, is limited to aligned sequences of 7,000 characters,
this includes the gaps in the aligned sequence. If you have the source
code it might be possible to increase this upper limit.

As an alternative you could try CLUSTALW (or the graphical version
CLUSTALX), however the larger the comparison the surface the longer the
alignment takes.

Michael Mitchell                 "Smoke me a kipper,
User Support                  I'll be back for breakfast."
Molecular Biology Software      Ace Rimmer, Test Pilot
+44 (0)171 269 3115                BBC-TV Red Dwarf           ENFJ

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