Dewit!

This is the first release candidate for TriFusion v1.0.0.

In this release a number of significant improvements were made to the performance and efficiency of the Process and Statistics modules. This resulted in up to 30x speed increase through most operations, particularly when dealing with thousands of alignments files (>50k files).

The other major improvement was in how partitions and substitution models are handled in TriFusion, particularly for output formats where they are required (MCMCtree, gphocs, ima2 and snapp). Partitions should now be defined, updated and modified correctly and seamlessly, even without user input.

The full list of changes is detailed below:

New Features

General

• Progressbar2 is now bundled with TriFusion to prevent import issues [0.5.3].
• Increased performance when updating app structures after loading alignment
  files into TriFusion [0.5.13].

Improvements

General

• Added animation for dropdown menus [0.5.17].
• Increased efficiency of filechoosers when opening directories with
  a great number of files [0.5.20].
• Improved item search in the main side panel [0.5.21].
• The order of partitions in the side panel and output files is now sorted
  according to the starting position of the position [0.5.23].
• Added EPS, PS, JPEG and TIFF options as figure formats [0.5.33].

Orthology

• Protein and nucleotide sequences exported by the Orthology module now have
  the same header for each taxa. This makes it easier for downstream processing
  of aligning concatenating, etc. [0.5.34].
• Added a backstage output file that makes the correspondance between the
  unique headers of ortholog groups and their original header in the proteome
  file [0.5.34].
• Added informative popups when comparing different group files with active
  filters and/or excluded taxa [0.5.34].
• Added usearch and mcl checks before executing the orthomcl_pipeline [0.5.35].

Process

• Refactored concatenation procedure increasing performance up to 29x in run
  time [0.5.4].
• Added automatic recognition of "?" as missing data symbols, in addition to
  "n" and "x" [0.5.5].
• Added option to invert selection of active Taxon/File buttons in the main
  side panel [0.5.6].
• Greatly improved performance when importing partition scheme for large
  alignments [0.5.7].
• Refactored Process backend to greatly improve performance of all operations,
  mainly when dealing with many input alignments. [0.5.10].
• New output format dialog design that informs which formats are available for
  main operations [0.5.11].
• Added check and warning when selecting output formats that are not valid
  for the current main operation [0.5.11].
• Several minor UI improvements [0.5.12].
• Increased memory efficiency of Process execution [0.5.14].
• Output files are now correctly generated when non-contiguous partitions
  are defined. These partitions are effectively merged before
  writing the output files [0.5.23].
• Added error message when there are no output formats after ignoring
  formats non-compliant with conversion/reverse concatenation [0.5.25].
• Added custom SNAPP output format extension [0.5.25].
• Added support for multiple sequence types (DNA and protein) for almost all
  operations [0.5.30].
• Major improvement of the partition and substitution model setup in
  certain output file formats (Nexus and Phylip) [0.5.30].
• Improved performance when toggling files/taxa on the side panel
  [0.5.39].
• Improved performance on alignment reading for Unix operating systems
  [0.5.40].

Statistics

• Improved legend positioning [0.5.1].
• Homogenized axis labels and title aesthetic style across plots [0.5.1].
• Color maps are dynamically selected based on the number of categories,
  resulting
  in more distinguishable color palettes [0.5.1].
• Improved sliding window line plots. These line plots are now smoothed with
  an interpolation, allowing for a much better and fine grained color
  transition [0.5.1].
• Improved dialogs and warnings for sliding window plots [0.5.27].

Bug fixes

General

• Fixed total data set information for taxon informative popup [0.5.16].
• Fixed text flickering for some informative popups [0.5.17].
• Fixed partition label update in side panel after merging or splitting [0.5.22].
• Fixed alignment counter for single partitions after splitting [0.5.23].
• Fixed occasional crash when canceling the loading of input files [0.5.31].
• Fixed removal of proteome files from selection in the side panel [0.5.33].

Orthology

• Handled exception when orthology filters result in no data to be
  plotted [0.5.6].
• Fixed import of some badly formatted group files in Orthology Explore
  section [0.5.24].
• Fixed issue where the end of the orthology search operation would hold
  indefinitely [0.5.28].
• Fixed minor issue with ortholog filter settings in explore section when
  proteome files are loaded [0.5.29].
• Fixed issue where plots with no data would prevent the generation of a full
  report [0.5.34].
• Fixed issues with orthomcl_pipeline that prevented the run from ending when
  invalid input files were present in the input directory [0.5.35].

Process

• Fixed 'ntax' parameter of NEXUS format when converting with custom active
  taxa sets [0.5.2].
• Fixed issue when reverse concatenating directly from an incorrect partitions
  file [0.5.8].
• Fixed issue when converting after specifying an output file for
  concatenation. [0.5.11]
• Fixed missing informative popups for inactive files/taxa [0.5.15].
• Fixed several issues of the partition scheme when using custom file data sets
  [0.5.18].
• Fixed issue with some Nexus badly formatted input files [0.5.19].
• Fixed several issues with partition and substitution model setup in Nexus
  and Phylip output formats [0.5.30].
• Fixed issue with overwrite/skip/cancel when executing process operations
  [0.5.32].
• Fixed issue with consensus using the first sequence method [0.5.37].
• Fixed issue preventing reverse concatenation from a single alignment
  when multiple alignments were provided [0.5.38].
• Fixed issues with partitions when removing alignment files [0.5.38].

Statistics

• Fixed color scheme for stacked bar plots that lumped together pairs
  of categories [0.5.1].
• Fixed issue where removing taxa from the active taxa group would not
  take effect on some operations of the Statistics module [0.5.36].