Linux Improvements:
    *  Autofinish on Linux can now handle larger amounts of memory
       (enough for most bacterial genomes).
 
    *  Gnome users:  the blank window problem is now fixed
 
 
Each of these new features is explained in README.txt supplied with
Consed.  These are just the highlights.  Consult README.txt for more
new features.
 
 
AutoPCRAmplify
 
    This is a new automated method of picking PCR primers to amplify
    particular regions.  It has been extensively used already.
 
New Autofinish Features:
 
    *  Autofinish is now easier to use because there is a point-and-click
       method of changing Autofinish parameters.  
 
    *  You can mark the end of a BAC and Autofinish will not try to
       extend past the end of the BAC.
 
    *  Smarter about which subclones to eliminate from using for read
       templates.
       
 
New Consed Features:
 
    *  Restriction Digest Display: graphically compares a real digest
       to the digest predicted from the sequence.  
 
       * Highlights mismatching fragments
 
       * The predicted fragments can be sorted by size (like a real
         gel), or sorted by position in the contig.
 
       * Also can print out a text version
 
       * Enables to to easily see the sequence of a particular
         location
 
       * Allows zooming in or out
 
    *  Bird's eye view of the assembly, showing pairs of forward and
       reverse reads that are consistent and inconsistent with the
       assembly.
 
       * Has various filters to eliminate clutter and pinpoint
         misassemblies
 
       * Indicates the confidence that the assembly is correct at a
         particular location
 
       * Allows zooming in or out
 
       * Shows contig order and orientation
 
    *  Consed now recalculates the quality values when modifying the
       assembly (adding new reads, joining, tearing, pulling a read
       out of a contig)
 
    *  You can now pull *any* read out of a contig, even if the read
       protrude out from the ends.
 
    *  Automatically scale traces so you don't have to keep changing
       the amplification as you move from one part of a read towards
       another, or as you compare traces from different kinds of
       sequencing machines
 
    *  Consed can now handle traces that are very long (up to about
       200Mb)
 
    *  When joining 2 contigs, there is a visual indication of which
       read came from which old contig
 
    *  Consed now allows as many tag types as you like
 
    *  If you wonder why Consed's primer picker didn't choose a
       particular primer, you can now ask it for the reason.
 
    *  Large speed up in Consed's primer picking in large assemblies
 
    *  Many user-friendly features
 
    *  Many bugs fixed