Changes in version 1.5.4                        

  - Added the function SubSetPairs that allows for easy trimming of
    predicted pairs based on conflicting predictions and / or prediction
    statistics.
  - Added the function EstimageGenomeRearrangements that generates
    rearrangement scenarios of large scale genomic events using the
    double cut and join model.

                        Changes in version 1.5.3                        

  - Added the function SequenceSimilarity and made improvements to
    runtime in DisjointSet.

                        Changes in version 1.4.1                        

  - Fixed a small bug in consensus scores in PairSummaries where
    features facing on different strands had their score computed
    incorrectly.

                       Changes in version 1.3.15                        

  - Changes to concensus score in PairSummaries.

                       Changes in version 1.3.14                        

  - Major changes to the PairSummaries function and minor changes to
    NucleotideOverlaps, ExtractBy, and FindSets. Adjustments to the
    model that PairSummaries calls on to predict PIDs.

                       Changes in version 1.3.13                        

  - ExtractBy function has been added. Allows extraction of feature
    sequences into XStingSets organized by the a PairSummaries object or
    the single linkage clusters implied by pairings within the
    PairSummaries objects.
  - DisjointSet function added to extract single linkage clusters from a
    PairSummaries object.

                       Changes in version 1.3.12                        

  - PairSummaries now computes 4-mer distance between predicted pairs.

                       Changes in version 1.3.11                        

  - PairSummaries now returns a column titled Adjacent that provides the
    number of directly adjacent neighbor pairs to a predicted pair. Gap
    filling code adjusted.
  - The function FindSets has been added and performs single linkage
    clustering on a pairs list as represented by vectors of integers
    using the Union-Find algorithm. Long term this function will have a
    larger wrapper function for user ease of access but will remain
    exposed.

                       Changes in version 1.3.10                        

  - NucleotideOverlap now passes it's GeneCalls object forward, allowing
    PairSummaries to forego inclusion of that object as an argument.

                        Changes in version 1.3.9                        

  - Minor vignette and suggested package changes.

                        Changes in version 1.3.8                        

  - PairSummaries now allows users to fill in specific matching gaps in
    blocks of predicted pairs with the arguments AllowGaps and
    OffSetsAllowed.

                        Changes in version 1.3.7                        

  - Adjustments to progress bars in both PairSummaries and
    NucleotideOverlap.
  - PID prediction models in PairSummaries adjusted.

                        Changes in version 1.3.6                        

  - Contig name matching has been implemented. Scheme expects users to
    follow NCBI contig naming and gff formats, accepting contig names
    from gffs directly, and removing the first whitespace and everything
    thereafter from FASTA headers. Contig name matching can be disabled
    if users wish, using the argument AcceptContigNames, but ensuring
    that the correct contigs in GeneCalls objects are matched to the
    appropriate contigs in Synteny objects are then the user's
    responsibility.

                        Changes in version 1.3.5                        

  - PairSummaries now translates sequences based on transl_table
    attributes provided by gene calls
  - PairSummaries now uses a generic model for predicting PID
  - gffToDataFrame now parses out the transl_table attribute

                        Changes in version 1.3.2                        

  - Minor changes to NucleotideOverlap
  - Major changes to PairSummaries - can now take in objects of class
    Genes build by the DECIPHER function FindGenes()

                       Changes in version 0.99.30                       

  - Vignette and help files edited for clarity

                       Changes in version 0.99.1                        

  - SynExtend submitted to Bioconductor
  - Added function gffToDataFrame
  - Added function NucleotideOverlap
  - Added function PairSummaries