### 0.5.0

#### Improvements

##### General

- Better handling of warning/error float checks.
- Improved warning dialog.
- Added multi selection for taxa and file data set groups with shift+clicking.
- Added label with selection information for data set group dialog.
- Added extension label in certain file choosers that require file name
definition.
- Added mcl (linux and windows 64bit) to distribution.
- Improve layout of floating errors, warnings and checks.
- Modifying previously created data set groups is now possible.

##### Process

- Interleave Phylip input format is now supported.
- Added text field to introduce split position when splitting partitions.
- More informative error message when importing inconsistent partition file.
- Usage of Threading or Multiprocessing changes dynamically depending on OS. This mainly means better performance on Unix.
- Custom directories for ZORRO weight files can now be provided.
- Added option to ignore (remove) sites with missing data when collapsing.
- Revamped the reverse concatenation dialog to make it more intuitive.
- A suffix can now be provided to the output files of the Conversion main
operation.

##### Orthology

- Added full report generation in HTML for Orthology graphical exploration.
- Added checks and troubleshooting for the two software requires in the
Orthology section (usearch and mcl).

#### Statistics

- Added percentage values to some summary statistics.
- Allele frequency spectrum plot now available in MAF proportions.
- Options in TriStats configuration file are now case insensitive.
- Added search field for summary statistics gene table view.

#### Bug Fixes

##### General

- Fixed double directory entry on secondary filechoosers.
- Fixed issue with Apply button in data set group creation.
- Fixed view queue button behaviour in Orthology and Process screens.
- Fixed crash with Add Bookmark keybinding in main filechooser.
- Fixed duplicate prevention routine when adding new partitions.
- Fixed faulty partition removal when removing an alignment with multiple
partitions.
- Fixed faulty behaviour with plot screen zoom using mouse wheel.
- Fixed interactive path references in secondary filechoosers.
- Fixed wrong taxa removal when removing files.
- Fixed issue with filechooser popup removal after trying to remove a bookmark.
- Fixed double directory entry on some filechoosers.
- Fixed issue when adding and removing bookmarks in secondary filechoosers.
- Fixed crash when selecting files from text file that contained non compliant entries.

##### Process

- Fixed bad loading of certain partitions schemes.
- More robust parser of nexus partitions files.
- Added several checks when splitting a partition manually.
- Fixed crash when importing data set group from file.
- Fixed issue with temporary directory creation when using the command line version.
- Fixed conversion of ZORRO weight files into integers (as RAxML requests).
- Fixed issue where ZORRO files were not correctly located.
- Fixed issue where ZORRO settings could be set without a valid suffix string.
- Fixed issue where ZORRO file checking was performed even when the switch
was OFF.
- Fixed faulty deactivation of user define partitions option in the reverse
concatenation dialog.
- Corrected phylip interleave output.
- Fixed issues with taxa removal for AlignmentList objects for command line
- Fixed Clear Options processing.
- Fixed issue with taxa filtering not working.
- Fixed issue when 0 alignments were filtered, even though at least one filter was active.
- Fixed issue with relative paths when loading files from terminal.
- Fixed wrong attribution of alignment files to partitions when importing from file.

##### Orthology

- Fixed awkward button behavior on Operations panel.
- Fixed issue with protein database name when exporting groups after a Search operation.
- Corrected minimum taxa representation proportion conversion.
- Fixed relatie paths issue when executing Orthology search.
- Fixed filter issues when loading new groups files after complete group removal.
- Fixed inability to export groups as nucleotide sequences.

##### Statistics

- Fixed active group selection when selecting the data set.
- Fixed issue with temporary directory creation when using the command line version.
- Fixed outlier removal.

### v0.4.12

This update is mainly to fix slow downs on subprocess spawning on Windows.

#### Improvements

##### General

- Migrated from multiprocessing to threading to spawn background tasks. This should result in a major performance increase in Windows and similar performance in Linux.

#### Bug Fixes

##### Orthology

- Removed Orthology Complement operation, for now.

##### Process

- Corrected process execution waiting dialog animation.


### v0.4.11

#### Improvements

##### Process

- More informative missing data filter dialog.

#### Bug Fixes

##### Process

- Fixed issue with locus size update after filtering missing taxa.
- Fixed duplicate detection in Process file loading.
- Fixed bug when adding partitions to current AlignmentList.
- Fixed exception handling when loading empty alignments.
- Fixed float calculations when filtering by taxa minimum.
- Added alignment cleaning for shelved alignments.
- Fixed issue that prevented correct sequence collapsing.
- Fixed issue with gap coding.
- Fixed temporary directory setting for reverse concatenation.
- Fixed 0 values for variation filters.
- Fixed issue when adding partitions to existing alignments.

### v0.4.0

##### New Features
- Added automatic calculation of summary statistics for the active data set when selecting the Statistics screen. All calculations are done in the background and can be canceled at any time. Summary statistics can be displayed for the overall data set or as a table with an entry for each gene

##### Improvements
- Added Warning class of float checks
- Duration of float checks can now be changed
- Replaced icon view filechoosers with list view filechoosers with multiple selection support
- Added refresh button to all filechoosers
- Added Cancel option when prompting for files with the same name as output
- Improved handling and termination of background process
- Improved protein filter settings text check in Orthology Search
- Improved ortholog filter settings text check in Orthology Search
- Added option to remove upper limit in gene copy ortholog filter
- Added option to provide minimum proportion of taxa for ortholog filter, instead of absolute value
- Added Ctrl+f keybinding to bring focus to find text input in secondary filechooser
- Completed Help texts in-App.
- Added information to orthoMCL pipeline log
- Added error handling when there is no unique field id on ortholog search
- Removed PIL dependency for converting plots to grayscale
- Prevented exit popup spamming.
- Added setup.py and re-structured TriFusion package.
- Added entry points for TriFusion GUI, and for command line versions of the three modules.
- Added more information on Statistics plots

##### Bug Fixes
- Corrected issue with table exportation in Statistics screen due to gray scale implementation
- Fixed issue with single gene plots for non active alignments
- Corrected behaviour of go to previous directory button in some filechoosers
- Fixed issues with Exit popup.
- Corrected bug with low e-values in Ortholog Search
- Corrected crash when loading a new project while calculating summary statistics
- Explicit disabling of stats plot type switch when a plot type is always inactive.
- Suppress import warnings for command line versions
- Handled secondary process exception when exiting the application
- Fixed issue that calls main twice

### v0.3.0

##### New Features
- Added Statistics plot with the cumulative distribution of missing genes for consecutive percentage values of missing data
- Added Statistics plot for the detection of sequence size outliers for genes and species
- Added Statistics plot for Allele Frequency Spectrum

##### Improvements
- Added a general file checking system for main process output
- Added support for Stockholm input and output formats
- Added support for GPhoCS output format
- Added support for automatic file loading via command line arguments when launching the app
- Added full support for TriSeq.py, the command line version of the Process module
- Added full support for orthomcl_pipeline.py, the command line version of the Orthology search module
- Added full support for TriStats.py, the command line version of the Statistics module
- Added support for wildcards in arguments for TriSeq.py and TriStats.py on windows
- Added data check decorator when calling Statistics related method that can handle different types of exceptions
- Added option to automatic convert all exported Statistics graphics to grayscale
- Added full support for TriOrtho.py, the command line version of the Orthology explore module

##### Bug Fixes
- Fixed issue with scrolling in Statistics Data exploration analyses panel
- Fixed crash when using keybindings to change to Statistics screen repeatedly
- Fixed path encoding issue when using Drag'N'Drop on Windows

### v0.2.0

##### Improvements
- Missing data and minimum taxa filters are now disassociated and can be executed separately

##### Bug Fixes
- Fixed issues with sequence case and interleave options in nexus output format
- Fixed missing imports
- Fixed faulty behaviour of shift+click on icon filechooser on Windows
- Fixed issue when writing output alignments with less than 90 characters in interleave format
- Fixed issue with number of output files when setting secondary operations

### v0.1.0