- Fixed reverse concatenation of non-contiguous and potentially overlapping partitions.
- Limited taxa buttons in side panel to improve performance in data sets with a large number of taxa (> 1000).
- Added support for non-contiguous partition files in RAXML format.
- Added support for reverse concatenation of multiple non-contiguous partitions without the need to specify the whole alignment in the partitions.
- Added character (nucleotide/residue) proportion for single genes plot. This new plot can be viewed in absolute counts or proportion character proportion.
- Added gene conservation plot for single genes.
- Taxa information popup from the side panel are now dynamically fetched and should be noticeable faster for large data sets.
- Added version option to all CLI interfaces via the "-v" or "--version" options.
- Improved handling and sanity checking of input and output directories for orthomcl_pipeline CLI interface.
- Automatic calculation of summary statistics has been disabled for data sets with a large number of taxa (> 1000). Calculation of summary statistics can still be triggered manually.
- Fixed orthomcl_pipeline error when the input proteomes where not properly sanitized (i.e., contain whitespace).
- Fixed issue where ortholog sequences were incorrectly retrieved from database under some circunstances.
- Fixed crash on stacked barplots due to deprecated vega colormaps.
- Fixed crash on sliding window plot for pairwise sequence similarity and segregating sites due to matplotlib update.
- Improved recognition of Nexus interleave information [1.0.0rc1.dev1].
- 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].
- 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].
- 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].
- 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].
- 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].
- 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].
- 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].
- 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].
- 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].