Alignment Software

George F.Mayhew mayhew at genome.wisc.edu
Fri Sep 29 11:52:35 EST 2000

Phred/Phrap for unix _are_ free to academic users, provided you fill out the
license forms.  You will need an assembly viewer/editor, too.  Consed or
GAP4 from the Staden package can be used. Phred/Phrap for _desktop_
architectures, like WindowsNT and Mac, are _not_ free, but can be gotten
from CodonCodes. Cross-compiling Phred/Phrap/Consed to Windows or Mac is not
trivial, and would require the services of an expert programmer to do it.
Buy the CodonCodes versions.

And if you have a cluster or multi-processor device, Gary Montry out at
South Pacific Software http://www.spsoft.com, has paralyzed Phrap and
Crossmatch.  We've seen huge performance increases in BAC assemblies with
this software

Phred/Phrap/Consed are excellent assemblers, but set-up is non-trivial,
especially if you wish to have multiple users on a single system. You need
to know some Perl if you don't want to use U.Washington's naming convention
for your clones.

The newest versions of SeqMan can handle 100,000 reads easily, will assemble
an entire bacterial genome random shotgun project (5+ MB), will use many
different types of input data, and works very well on Windows environments.
Our lab is a beta site for the company, and we've seen some very encouraging
new features come through recently.  Contact DNAstar sales (608-258-7420) to
find out when the new release is due out.

I haven't spoken to Howard Cash and his group at GeneCodes in quite some
time, and can't comment on his product, but previously it kept pace with
SeqMan development, with some file management and feature pluses going for

GCG also has a new addition to it's suite of X-windows products, called
SeqMerge.  It's still in its infancy, but looks promising, at least as an
editor. It's pricey (~12,000 per year, I think), but plugs right into an
existing GCG install.

My 2c worth.  Hope it's helpful.


George F. Mayhew
Sr. Instrumentation Specialist
UW Genome Projects
Laboratory of Genetics
College of Agricultural and Life Sciences and the Medical School
University of Wisconsin - Madison
445 Henry Mall, Madison, WI 53706
Phone: 608-262-2534
Fax:   608-263-7459
Email: mayhew at genome.wisc.edu
URL:   http://www.genome.wisc.edu/~mayhew/

"Graham Clark" <gc1 at scarba.sanger.ac.uk> wrote in message
news:8qvl29$9e0$1 at mercury.hgmp.mrc.ac.uk...
> Jannik Helweg-Larsen <jhelweg at inet.uni2.dk> writes:
> > Phred-phrap is NOT free according to codoncode.com: prices for
> > Academic users are between 880-920US$ according to operating system
>    It may still be possible to get it from
> The pages there certainly imply that it is, although they may of course be
> of date. It doesn't mention payment for non-profit academic users,
> this may of course be an omission rather than an accurate summary. Worth
> trying, though, I'd have thought.
> Graham.
> --

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