[Bioperl-l] the binary formerly known as WU-BLAST (Was: experimental Bio::Search::Tiling implementation)

Robert Buels rmb32 at cornell.edu
Tue May 19 23:48:55 EDT 2009

Are the developers of RepeatMasker and RepeatModeler aware of this 
availability problem?  Perhaps they have some ideas?

I'm CCing R. Hubley, whose email is listed first in the RepeatModeler 
source file headers.


Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

Erich Schwarz wrote:
> On Tue, 19 May 2009, Mark A. Jensen wrote:
>> Jason's usual remarks involve the use of wu-blast with the --links
>> option, and wu-blast has recently turned commercial and is
>> evidently costly to obtain.
>     Is AB-BLAST (the putative successor to WU-BLAST) obtainable
> *anywhere* on any terms?  The only information I've been able to get
> has been this rather unhelpful site:
>     http://www.advbiocomp.com/
>     http://www.advbiocomp.com/faq.html
> whose FAQ has been claiming availability "soon" for the last half
> year.
>     I wouldn't care, except that [1] I belatedly moved my heavier
> computing jobs from an i686 Linux box to an x86_64 megabox, and [2]
> a repeat-finding package I will probably need to be running fairly
> often in 2009-2010:
>     http://www.repeatmasker.org/RepeatModeler.html
> relies on WU-BLAST i686 binaries which don't work terribly well on
> x86_64, and for which I cannot get x86_64 replacements.
>     Sorry to go on a tangent, but I'd appreciate any information
> anybody has about getting WU-BLAST effectively replaced.
> --Erich
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