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].