RELEASE-NOTES

RepeatModeler 1.0.11
====================
  - Bugfix release. Avoid bailing if Refiner could not produce a consensus 
    from the family sequence set.

RepeatModeler 1.0.10
====================
  - Bugfix release. Fixes a bug that will cause RepeatModeler to exit 
    if no new repeats are detected after round-2. This may happen if the
    sample size is small enough or contains a repeat-poor set of sequences
    and may not reflect the chance that repeats will be found in later rounds.
    Typically new repeats are found in all rounds of RepeatModeler.

RepeatModeler 1.0.9
===================
  - RepeatModeler employs a genome sampling approach that is based
    on a random number generator. In this release of RepeatModeler
    we print out the random number generator seed at the start of 
    a run.  This number can be used with the "-srand ####" flag in future
    runs to exactly reproduce the samples taken from a given database.

  - The final output files are now placed in the same directory as
    the input database.  

  - An additional output file is now generated containing the seed 
    alignment for each discovered family.  This alignment is the source
    of the final consnesus and is stored in a Dfam compatible Stockholm
    file.  The new output files are named <database_name>-families.fa and
    <database_name>-families.stk.
    
  - Support for Dfam_consensus has been built into this release. Two
    utilities dfamConsensusTool.pl and renameIds.pl can be found in the
    RepeatModeler util/ directory.  The dfamConsensusTool script enables
    one to upload curated seed alignments to the open Dfam_consensus 
    database from the command line.  The renameIds script simplifies
    the process of coming up with unique identifiers for a set of 
    RepeatModeler generated families given a naming template.

RepeatModeler 1.0.8
===================
  - New "-recoverDir <dir>" option.  This allows RepeatModeler to 
        restart where it left off after a failure occurs.  
  - BLAST searches can now be run in parallel on a shared memory 
        multiprocessor machine.  The new "-pa #" option is used to
    specify how many parallel searches to start up at any one time.

RepeatModeler 1.0.7
===================
  - Added support for new RMBlastn version 2.2.27
      - TRFMask updated to work with the new RepeatMasker 4.0 release.
          - New viewMSA.pl utility