RMBLAST README

 Overview
 ========
 RMBlast is a RepeatMasker compatible version of the standard
 NCBI BLAST suite.  The primary difference between this 
 distribution and the NCBI distribution is the addition of a new
 program "rmblastn" for use with RepeatMasker and RepeatModeler.

 RMBlast supports RepeatMasker searches by adding a few 
 necessary features to the stock NCBI blastn program.  These
 include:

   - Support for custom matrices ( without KA-Statistics ).
   - Support for cross_match-like complexity adjusted scoring.
     ( Cross_match is Phil Green's seeded smith-waterman search 
       algorithm: www.phrap.org ) 
   - Support for cross_match-like masklevel filtering.
 
 Caveats
 =======
 Changes to the core ncbi algorithms were minimized and attempts were 
 made to shield the other standard NCBI programs included in this distrubtion
 from these changes.  However, we recommend that this package 
 be installed in a distinct directory from the standard NCBI 
 distribution on your system.  This will minimize the chance that
 packages other than RepeatMasker or RepeatModeler use this installation.
 This distribution is only intended for use with RepeatMasker/RepeatModeler.

 Credits
 =======
 Arian Smit - Institute for Systems Biology
 Robert Hubley <rhubley@systemsbiology.org>  - Institute for Systems Biology
 Jeb Rosen <jeb.rosen@systemsbiology.org> - Institute for Systems Biology
 
 National Center for Biotechnology Information ( NCBI )
 
 And special thanks to:
   Tom Madden,
   Denis Vakatov,
   Aaron Ucko,
   Ning Ma, and
   George Coulouris 
 at NCBI for allowing us to bug them with questions about
 the BLAST source code, assistance with finding resources,
 and lending an ear to tired programmers.

 This work is funded by NHGRI grant # RO1 HG002939-13

 Installation
 ============

 This copy of the README was distributed with the binary releases
 of rmblast provided by Institute for Systems Biology.

 Full installation instructions for RMBlast are provided at

 http://www.repeatmasker.org/RMBlast.html

 Feedback
 ========
 Please visit www.repeatmasker.org to submit questions or feedback
 for us.
