WHAT IS NEW IN CONSED 14.0

Itanium (64-bit linux) is now available.

Assembly View
    Sequence matches are shown, and can be used to make joins.

    Can show restriction digest cut sites.  More probably coming on
    this.

    Tags Can be Shown.  You can customize which tag types are shown.
    Clicking on a tag shows more information about it and displays
    that location in the Aligned Reads Window.

    Can more easily specify which contigs to show.

Show Traces for All Reads
    If you are examining traces hundreds of reads deep, then Consed
    will now show you the reads in batches of 100 at a time.  It will
    optionally not show reads that have no base at the cursor position,
    have no trace near the cursor position, or that have a user-specified
    tag at the cursor position.  This helps focus on the reads you need to
    look at.
    
    There were some bugs with this feature--I believe they are all
    fixed.

AutoPCRAmplify
    Can now be used in cases in which you only have a fasta file of
    the region to amplify, such as when you download the sequence
    from Genbank or UCSC.

    Now more likely to find pcr primer pairs.

    Can optionally use a fixed primer for one end, such as when using
    a transplice leader sequence.

    User feedback helped me improve the criteria for rejecting PCR
    primer pairs.

Improvement for Huge Assemblies
    You can concatentate all of the phd files into a single file and
    delete the many phd files.

    You can type in the contig name rather than selecting it from a
    list--good if the list is hundreds of contigs long.

    You can filter which ace files you want displayed--useful if there
    are a huge number of ace files.

Custom Data Within Tags
    Consed has always allowed user-defined tag types.  Now Consed
    allows you to defined fields within user-defined tags.  For
    example, you might define an exon tag with a field which is a
    pointer to a gene tag.

Miniassemblies
    Users have found they sometimes only recognize they made a mistake
    after starting a miniassembly.  But they couldn't stop it.  Now
    there is a "Cancel Miniassembly" button.

Autofinish
    To prevent Autofinish from trying to do pcr with a particular
    contig-end, there is now a doNotDoPCR tag that Autofinish will
    obey.

Bugs fixed
    Macosx Autofinish crash
    Linux AutoPCRAmplify crash
    One caused a corrupted ace file.