Release notes for Blixem 2.4, 970618. (Relative to version 2.3, 960305.)
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   HEADLINES:
   ----------

 * Changed FTP site: ftp://ncbi.nlm.nih.gov/pub/esr/MSPcrunch+Blixem

 * Support for gapped Wublast 2.0 output. This requires MSPcrunch 2.1.  
   Insertions in the query sequence are shown as dots in the subject
   while insertions in the subject are removed by MSPcrunch and are
   highlighted in Blixem by color (red).  Subject insertions are
   marked either by a lower case residue after the insertion (default
   MSPcrunch -q) or by a number (=size of insertion) (MSPcrunch -N
   -q).  Subject insertions can not be displayed as in most cases they
   would ruin the alignment (trust me).  For Blixem/ACEDB users,
   MSPcrunch -4 will output gapped matches as a sequence of ungapped
   segments, analogous to the HMM-match format.  Some work is needed
   on ACEDB to make it call Blixem with gapped matches.
   
 * New Settings menu option "Show sequence descriptions" displays the DEFline
   of the subject under each match.  This requires MSPcrunch 2.1.

 * The color of matching residues is now settable in the Settings window.

 * For those who use Blixem in situations where a single input stream
   is preferable (e.g. via the Web), it is now possible to pipe both
   the query sequence and the MSPs at once.  The format should be:
   First line: query name.  Second line: query sequence.  The rest:
   normal seqbl (MSPcrunch -q) output.  Pipe this to "blixem - -"


   Bugfixes
   ------------------------

 * After squashing matches, the old sorting is now restored.

 * More robust searching for a WWW brower for efetching.

 * Start-up sorting by Identity (-si).

 * Big Picture MSPs on reverse strand were sometimes bugged in (t)blastx mode.


Erik Sonnhammer