Release 2.2.7
=============
    - [BUG FIX] More intuitive behavior for the maximum subproblem option from
                the GUI. There are two controls for the maximum subproblem
                used during tree decomposition, frac and size. Both of these
                have default values, and the larger of the two is used to
                determine the maximum subset size during decomposition. This
                caused confusion when using the GUI, because the selected
                option was ignored if it was smaller than the default for
                the alternative option. The GUI now explicitly configures
                BOTH options as per the user's radio-button selection, so
                that what the user sees is what they get. In short, always
                check the configuration file reported by SATe! This will
                tell you exactly what SATe is doing.

Release 2.2.6
=============
    - [CHANGES] RNA sequence data is now fully supported. There was some
                inconsistency in previous versions as to whether RNA data was
                allowed to run (under some versions and configurations it was
                allowed to run as DNA data). This version internally converts
                RNA input to DNA and then converts the final results back to
                RNA.
    - [CHANGES] Updated the alignment length check that determines which
                MAFFT algorithm to use for alignment. Previously this checked
                the alignment length, it now uses the maximum unaligned
                sequence length.
    - [CHANGES] Better error messaging when input sequence labels conflict
                with tip labels of a user-provided starting tree. The error
                message now reports the problem and lists all of the mismatched
                labels.
    - [CHANGES] This version gives explicit warning messages when the user
                specifies a max subproblem argument that is equal to or greater
                than the number of tips. Under these conditions, the SATe
                algorithm is not invoked. The warning makes this more clear to
                the user.
    - [CHANGES] Many tests added to the test suite.

Release 2.2.5
=============
    - [BUG FIX] Fixed directory cleanup error messages introduced with release
                2.2.4. SATe can now remove temporary directories without these
                annoying error messages. This bug did not affect analyses.
    - [BUG FIX] Fixed tree-decomposition recursion bug introduced with release
                2.2.4. During some recursions, multiple sate aligner jobs would
                attempt to create the same temp directory, causing the analysis
                to exit with an error. This release corrects this problem. Any
                results obtained from 2.2.4 should not be effected by the bug,
                because this bug always resulted in a crash.

Release 2.2.4
=============
    - [BUG FIX] Fixed temp directory path depth problem in Windows when using
                "longest" decomposition. Previous versions created a nested
                temp file directory that mirrored the tree decomposition. In
                Windows, if the tree had enough long terminal branches, the
                temp files got too long for the OS. The temp file structure
                has been changed to avoid this problem.
    - [BUG FIX] Fixed problem with too many open files when multi-locus
                analyses had many loci.

Release 2.2.3
=============
    - [CHANGES] MUSCLE is now the default merger tool.
    - [CHANGES] Centroid is now the default decomposition strategy.
    - [CHANGES] More sample data and output files bundled.

Release 2.2.2
=============
    - [BUG FIX] Previous version had used the "Centroid" decomposition even when
                the user specified "Longest."
    - [BUG FIX] Multiple issues dealing the handling very small subsets of taxa.
                These arise frequently in the "longest" edge decomposition, but
                are rare when using centroid decomposition.
    - [BUG FIX] Input sequences with all gaps no longer create problems (this
                can reasonably occur in multi-locus runs).
    - [CHANGES] FastTree binary in Mac bundle is compiled for more
                architectures.
    - [CHANGES] Updated documentation.
    - [CHANGES] RAxML user-specified arguments implemented in CLI.
    - [CHANGES] Post-processing RAxML search now uses
                start_tree_search_from_current boolean to determine whether to
                use the tree resulting from the SATe algorithm as starting tree.
    - [CHANGES] Updated bundled data.
    
Release 2.2.1
=============

    - [BUG FIX] Minor fix to initial GUI display. Initial "Model" options now
                correspond to FastTree options.
    - [CHANGES] updated documentation in README and FAQ.

Release 2.2.0
=============

    - [BUG FIX] No longer uses 'N' for missing taxa in multi-locus mode, which
                caused problems with multi-locus amino acid analyses with
                missing taxa.
    - [CHANGES] Fasttree is now bundled with SATe.
    - [CHANGES] New option to automatically set defaults based on size of
                dataset.
    - [CHANGES] Several default settings changed.

Release 2.1.0
=============

    - [BUG FIX] No longer write out duplicate sequence entries in final
                alignment output.
    - [CHANGES] Do not clean up files and directories in temporary working
                directory not created by SATe.
    - [BUG FIX] Check for gamma score in output file before using value in log
                file.

Release 2.0.3
=============

    - Fix for not terminating correctly in SATE-II-fast mode.
    - Allow specification of memory to be allocated to JVM when running Opal
      [NOTE: default memory allocation is now 1024MB instead of 2048MB].
    - Default to SATE-II-fast mode instead of SATE-II-ML.
    - SATE-II-ML defaults to 10 iterations instead of 100.

Release 2.0.2b
==============

    - Fix for multilocus analysis with non-equal leaf-sets.
    - Fix for allowing SATe application bundle to be run from directories with
      non-alphanumeric characters in path.

Release 2.0.1b
==============

    - Support for multilocus analysis.
    - `pairalign` (MAFFT) is not run if sequences are > 10K characters. This
      configuration has not been benchmarked.
