--- Release notes SplitsTree6 V6_3_10 (Fri, 19 Apr 2024): --- - bug fixes in PDF export --- Release notes SplitsTree6 V6_3_9 (Thu, 18 Apr 2024): --- - bug fixes median joining network viewer --- Release notes SplitsTree6 V6_3_8 (Thu, 18 Apr 2024): --- - bug fixes in pie chart resizing --- Release notes SplitsTree6 V6_3_7 (Wed, 17 Apr 2024): --- - added zoom to data button to world map - put user documentation on GitHub --- Release notes SplitsTree6 V6_3_6 (Sat, 13 Apr 2024): --- - minor fixes - more work on PDF export - added -d and -s command line options - simplified consensus tree algorithm --- Release notes SplitsTree6 V6_3_5 (Fri, 12 Apr 2024): --- - minor fixes - more work on PDF export --- Release notes SplitsTree6 V6_3_4 (Thu, 11 Apr 2024): --- CRITICAL UPDATE - previous installer broken - changed name to SplitsTree App - updated to Java 22 --- Release notes SplitsTree6 V6_3_3 (Thu, 11 Apr 2024): --- - changed name to SplitsTree App - added world map view for traits data with world coordinates - fixed bugs in PDF and SVG export --- Release notes SplitsTree6 V6_3_2-beta (Mon, 8 Apr 2024): --- - added LSA tree and blob tree algorithms --- Release notes SplitsTree6 V6_3_1-beta (Tue, 26 Mar 2024): --- - bug fixes - UI update --- Release notes SplitsTree6 V6_3_0-beta (Tue, 19 Mar 2024): --- CRTICAL update - fixed bug that prevented program for running correctly - major refactoring of user interface --- Release notes SplitsTree6 V6_2_2-beta (Thu, 8 Feb 2024): --- - added QR codes - added ALTS networks algorithm (not working correctly yet) --- Release notes SplitsTree6 V6_2_1-beta (Thu, 16 Nov 2023): --- - simplified UI --- Release notes SplitsTree6 V6_2_0-beta (Thu, 16 Nov 2023): --- - simplified UI - fixed bug in visualization of confidence - fixed bug in Hamming ambiguous states - handle ignore .. --- Release notes SplitsTree6 V6_1_16-beta (Sun, 1 Oct 2023): --- - improved svg and pdf export - now using maven to build project - added licenses - removed tSNE because not compatible with maven and Java 17 --- Release notes SplitsTree6 V6_1_15-beta (Fri, 29 Sep 2023): --- - fixed bugs in PDF and SVG export --- Release notes SplitsTree6 V6_1_14-beta (Fri, 22 Sep 2023): --- - fixed bug that caused parsing of trees to fail when using non-rich Newick format with confidence values --- Release notes SplitsTree6 V6_1_13-beta (Tue, 12 Sep 2023): --- - added BlobTree algorithm to splits filter --- Release notes SplitsTree6 V6_1_12-beta (Mon, 11 Sep 2023): --- - fixed bug in rooted network algorithm choice - fixed bugs in transfer visualization --- Release notes SplitsTree6 V6_1_11-beta (Mon, 11 Sep 2023): --- - fixed recent bug in consensus calculation --- Release notes SplitsTree6 V6_1_10-beta (Tue, 5 Sep 2023): --- - added options to plain text output of distances --- Release notes SplitsTree6 V6_0_35-beta (Thu, 24 Aug 2023): --- - median joining and spanning network visualization now save user dragged nodes and node labels, and dragging of nodes and node labels is undoable - implemented GML export for median network --- Release notes SplitsTree6 V6_0_34-beta (Wed, 23 Aug 2023): --- - reverted to using Neighbor-net code for computing cycle for imported splits (is faster on very large sets of splits) - if a Newick string has node comments that are all numerical then these numbers are interpreted as edge confidence values (to allow import of some RAxML files.) --- Release notes SplitsTree6 V6_1_9-beta (Thu, 10 Aug 2023): --- - fixed bug that prevented of importing of data when there are multiple possible parsers and one failed --- Release notes SplitsTree6 V6_1_8-beta (Wed, 2 Aug 2023): --- - fixed bug that caused connector lines in Tanglegram to be incorrectly positioned or to disappear --- Release notes SplitsTree6 V6_1_7-beta (Fri, 21 Jul 2023): --- - fixed bug that ignored weights option when exporting trees to newick format. - Added code to allow external running of the ALTS algorithm --- Release notes SplitsTree6 V6_1_6-beta (Wed, 12 Jul 2023): --- - replaces previous release that was unable to start due to a configuration error - uses Java 20 runtime --- Release notes SplitsTree6 V6_1_5-beta (Wed, 12 Jul 2023): --- - fixed bug that prevented correct identification of files containing newick trees when the file suffix was non-standard - improved handling of missing values and saturated sites in distance calculations: if all calculated values are below 1, then missing values are set to 1, otherwise, missing values are set to 1.1 times the largest value calculated, and the rounded to the nearest value of the leading digit , like 700, say, (to make it easy to recognize which matrix entries have been replaced in this way) --- Release notes SplitsTree6 V6_1_3-beta (Mon, 10 Jul 2023): --- - removed new cycle calculation algorithm due to implementation problems that need fixing , --- Release notes SplitsTree6 V6_1_2-beta (Wed, 5 Jul 2023): --- - changed neighbor-net default to ActiveSet - added max wall-clock time option to Run-Workflow program - bug fixes , --- Release notes SplitsTree6 V6_1_1-beta (Thu, 29 Jun 2023): --- - fixed issue that SVG export of images not recognized by Inkscape --- Release notes SplitsTree6 V6_1_0-beta (Wed, 28 Jun 2023): --- - Major improvement of new neighbor-net algorithms - Now supports export of objects to PDF and SVG - this was implemented from first principles, please report any bugs that you encounter! --- Release notes SplitsTree6 V6_0_33-beta (Tue, 27 Jun 2023): --- - fixed some issues with PDF output --- Release notes SplitsTree6 V6_0_32-beta (Mon, 26 Jun 2023): --- - first version of export image to PDF with objects, not pixels - fixed label layout bug in Densi-tree - fixed bug in split-newick --- Release notes SplitsTree6 V6_0_31-beta (Mon, 12 Jun 2023): --- - removed newly introduced bug in genome reference search --- Release notes SplitsTree6 V6_0_30-beta (Mon, 5 Jun 2023): --- - import of Newick trees now captures gene names, if present - import of Newick trees now captures comments, and this will be used in future releases - fixed issues that caused no planar networks to be shown with a poor circular layout - fixed bug in enabling/disabling of menu items - added explicit call to SplitsTree4 version of neighbor-net - some bugs in new NNet algorithms fixed, but there is still a problem that is significantly degrading the sped of the new algorithms --- Release notes SplitsTree6 V6_0_29-beta (Thu, 20 Apr 2023): --- - added *fit* calculation to consensus methods. --- Release notes SplitsTree6 V6_0_28-beta (Fri, 14 Apr 2023): --- - fixed bug that prevents genome analysis window from opening sometimes --- Release notes SplitsTree6 V6_0_27-beta (Thu, 13 Apr 2023): --- - added export image button and menu item - fixed bug that caused caused editor to fail on windows - addressed bug that prevented paste into editor - tried to fixed bug that prevents genome analysis window from opening sometimes - uploaded new version of gtdb_rep_k21_s10000.db.zip, which is necessary because location of genomes at NCBI has changed - fixed bugs in split-newick parser and writer --- Release notes SplitsTree6 V6_0_26-beta (Tue, 11 Apr 2023): --- - added export image button and menu item --- Release notes SplitsTree6 V6_0_25-beta (Fri, 31 Mar 2023): --- - fixed an issue with importing nexus files containing partial trees - fixed an issue in parsing of split newick data when taxon names are surrounded by single quotes --- Release notes SplitsTree6 V6_0_24-beta (Fri, 24 Mar 2023): --- - first experimental version of newick format for split networks - fixed mash sketch calculation tool problems --- Release notes SplitsTree6 V6_0_23-beta (Wed, 8 Mar 2023): --- - added *list pairs of trees that have 1-rSPR distance* analysis report - allow input trees to have numerical taxon labels on leaves --- Release notes SplitsTree6 V6_0_22-beta (Sat, 4 Mar 2023): --- - added citations to ecological indices calculations - added Phi test - started writing online documentation --- Release notes SplitsTree6 V6_0_21-beta (Fri, 3 Mar 2023): --- -new implementation of neighbor-net cycle calculation - added new example --- Release notes SplitsTree6 V6_0_20-beta (Wed, 1 Mar 2023): --- - implemented support for the saving and reopening of report blocks --- Release notes SplitsTree6 V6_0_19-beta (Wed, 22 Feb 2023): --- - results of analysis are now written to a *Report* block --- Release notes SplitsTree6 V6_0_18-beta (Mon, 20 Feb 2023): --- - more work on phylogenetic diversity indices --- Release notes SplitsTree6 V6_0_17-beta (Fri, 17 Feb 2023): --- - renamed fair proportion to evolutionary distinctiveness - added phylogenetic diversity on split networks - added Shapley value calculation for split networks - at present the results of the diversity calculations are reported to the Message Window, this will be improved in one of the next releases --- Release notes SplitsTree6 V6_0_16-beta (Thu, 16 Feb 2023): --- - renamed fair proportion to evolutionary distinctiveness -added phylogenetic diversity on split networks --- Release notes SplitsTree6 V6_0_15-beta (Thu, 16 Feb 2023): --- -added items in analysis menu for computing phylogenetic diversity and fair proportion values on trees and networks (when present in the tree view, not tree pages or tanglegrams) --- Release notes SplitsTree6 V6_0_14-beta (Tue, 14 Feb 2023): --- - fixed bug in 1-rSPR calculation, again --- Release notes SplitsTree6 V6_0_13-beta (Tue, 14 Feb 2023): --- - fixed bug in 1-rSPR calculation --- Release notes SplitsTree6 V6_0_12-beta (Thu, 9 Feb 2023): --- - improved code that extract trees from a rooted network --- Release notes SplitsTree6 V6_0_11-beta (Tue, 7 Feb 2023): --- - added edge-scaling option to super network and filtered super network - some work on neighbor-net --- Release notes SplitsTree6 V6_0_10-beta (Tue, 31 Jan 2023): --- - added edge-scaling option to super network and filtered super network --- Release notes SplitsTree6 V6_0_9-beta (Mon, 30 Jan 2023): --- - greedy consensus methods now use the same sorting every time, no random fluctuations - fixed a number of minor bugs associated with the input editor window - added confidence filter to treefilter2 --- Release notes SplitsTree6 V6_0_8-beta (Tue, 24 Jan 2023): --- - greedy consensus methods now use the same sorting every time, no random fluctuations --- Release notes SplitsTree6 V6_0_7-beta (Sun, 15 Jan 2023): --- - fixed recently introduced bug that prevented use of densi-tree view - now allow rooted networks as input to densi-tree view, but don’t draw networks in densi-tree view yet --- Release notes SplitsTree6 V6_0_6-beta (Sun, 15 Jan 2023): --- - consensus trees and networks can now be computed for rooted networks, not just rooted trees - added new export format *NexusWithTaxa” to RunWorkflow --- Release notes SplitsTree6 V6_0_5-beta (Thu, 12 Jan 2023): --- - added more examples - fixed bug that sometimes prevented all taxa being found when importing newick trees --- Release notes SplitsTree6 V6_0_4-beta (Thu, 12 Jan 2023): --- - Renamed to SplitsTreeCE - Added command-line tools - Fixed bug in workflow export - Newly introduced exception in neighbor-net removed - Explicitly reject multi-labeled trees - Input editor now scrolls to error line --- Release notes SplitsTree6 V6_0_3-beta (Wed, 11 Jan 2023): --- - fixed issue in calculation of consensus tree in densi-tree visualization --- Release notes SplitsTree6 V6_0_2-beta (Mon, 9 Jan 2023): --- - added threshold percent to consensus splits and consensus outline - turned off anti consensus and confidence network, as they don’t seem to work properly --- Release notes SplitsTree6 V6_0_1-beta (Wed, 4 Jan 2023): --- - added a number of new options to DensiTree visualization --- Release notes SplitsTree6 V6_0_0-beta (Wed, 4 Jan 2023): --- - now can import a list of tree names to attach to trees - made GitHub repository public - First beta release of SplitsTree CE --- Release notes SplitsTree6 V0_4_4-alpha (Wed, 7 Dec 2022): --- - fixed bug that prevented parsing of some rooted networks in extended Newick format --- Release notes SplitsTree6 V0_4_3-alpha (Mon, 28 Nov 2022): --- - added vertical *block increment* to alignment viewer: clicking in the vertical scroll track will scroll by one page up or down - fixed update URL --- Release notes SplitsTree6 V0_4_2-alpha (Sun, 27 Nov 2022): --- - added horizontal *block increment* to alignment viewer: clicking in the horizontal scroll track will scroll by one page to the left or right - fixed bug that caused coordinates to be off sometimes in alignment viewer - fixed bug that caused file to be opened in existing document despite the input editor already being open --- Release notes SplitsTree6 V0_4_1-alpha (Fri, 25 Nov 2022): --- CRITICAL BUG FIX - the previous update introduced a bug that caused algorithm settings to be ignored --- Release notes SplitsTree6 V0_4_0-alpha (Tue, 22 Nov 2022): --- - menu items how have check marks to indicate which are active, and are disabled if not applicable - added reset buttons for densi-tree colors - fixed bugs and cleaned up gene content distances --- Release notes SplitsTree6 V0_3_9-alpha (Wed, 26 Oct 2022): --- - Fixed some exceptions that got thrown when viewing trees - Added options for changing edge widths and colors in densi-tree visualization --- Release notes SplitsTree6 V0_3_8-alpha (Wed, 21 Sep 2022): --- - Fixed bugs that prevented processing of character blocks that contain a CHARSTATELABELS statement. --- Release notes SplitsTree6 V0_3_7-alpha (Tue, 20 Sep 2022): --- - Implemented Sets block: allows one to specify tax-sets and char-sets for selection in nexus files. - Fixed bug that caused traits behave incorrectly when hiding taxa --- Release notes SplitsTree6 V0_3_6-alpha (Fri, 16 Sep 2022): --- - Improved performance of alignment viewer --- Release notes SplitsTree6 V0_3_5-alpha (Fri, 2 Sep 2022): --- - Fixed following issue: Release 0.3.4-alpha failed to start on some systems --- Release notes SplitsTree6 V0_3_4-alpha (Fri, 2 Sep 2022): --- - Added implementation of GTDB-based phylogenetic context analysis dialog. --- Release notes SplitsTree6 V0_3_3-alpha (Tue, 30 Aug 2022): --- - fixed some bugs in undo/redo --- Release notes SplitsTree6 V0_3_2-alpha (Tue, 30 Aug 2022): --- - more work on densi-tree - added internal features --- Release notes SplitsTree6 V0_3_1-alpha (Mon, 22 Aug 2022): --- - removed some neighbor-net debugging output - greedy tree algorithm now also maintains confidence values, if given --- Release notes SplitsTree6 V0_3_0-alpha (Mon, 22 Aug 2022): --- - implemented the Booth and Luecker (1976) PQ-tree algorithm - It is used to produce a better layout of densi-trees - it is used to added a new greedy-outline consensus method that contains a consensus outline for a a set of input trees --- Release notes SplitsTree6 V0_2_6-alpha (Wed, 27 Jul 2022): --- - Added rotation and reversing of children or subtrees below a node for trees (but not rooted networks) --- Release notes SplitsTree6 V0_2_5-alpha (Tue, 26 Jul 2022): --- - fixed bug in undock tab that caused some colors to disappear - when using find for a single taxon, will automatically scroll to found item - find and replace comboboxes now share terms across different windows and dialogs --- Release notes SplitsTree6 V0_2_4-alpha (Sat, 23 Jul 2022): --- - added new densi-tree visualizations - fixed bugs associated with notifications - improved syntax highlighting --- Release notes SplitsTree6 V0_2_3-alpha (Fri, 15 Jul 2022): --- - bug fixes --- Release notes SplitsTree6 V0_2_2-alpha (Fri, 15 Jul 2022): --- - Deployed Darias code for syntax highlighting in input and display tabs - Input and display tabs now scroll to found text when finding or replacing --- Release notes SplitsTree6 V0_2_1-alpha (Sun, 10 Jul 2022): --- - Bug fixes --- Release notes SplitsTree6 V0_2_0-alpha (Sun, 10 Jul 2022): --- - implemented support for *rich Newick* format - implemented label edges by weight, confidence or probabilities - read weights, confidences and/or probabilities on reticulate edges - improved cluster-based selection in trees - fixed bug in window sizing - fixed issues with rerooting (Known bugs: sometimes tree is not shown on reopening, status of alignment node in workflow is not updated) --- Release notes SplitsTree6 V0_1_8-alpha (Mon, 27 Jun 2022): --- - fixed selection bug in densi-tree viewer - now ignores options statement in characters block --- Release notes SplitsTree6 V0_1_7-alpha (Sun, 26 Jun 2022): --- - fixed bug that caused some context menus to contain duplicate items --- Release notes SplitsTree6 V0_1_6-alpha (Sat, 25 Jun 2022): --- - added info to breadcrumbs bar - fixed bug that caused larger files not to be put into the recent files menu - fixed missing md5sums.txt file issue --- Release notes SplitsTree6 V0_1_5-alpha (Fri, 24 Jun 2022): --- - fixed bug that caused tanglegrams to fail on larger examples. --- Release notes SplitsTree6 V0_1_4-alpha (Fri, 24 Jun 2022): --- - densi-trees now show consensus tree --- Release notes SplitsTree6 V0_1_3-alpha (Thu, 23 Jun 2022): --- preliminary implementation of densi-trees --- Release notes SplitsTree6 V0_1_2-alpha (Mon, 20 Jun 2022): --- - moved PCoA and TSne to Analysis menu - better label layout for PCoA and TSne --- Release notes SplitsTree6 V0_1_1-alpha (Sun, 19 Jun 2022): --- - fixed bad bug in presentation mode --- Release notes SplitsTree6 V0_1_0-alpha (Sun, 19 Jun 2022): --- - export dialog is now modal - added BinaryToSplits and DnaToSplits algorithms - selecting algorithm from context menu in workflow tree now also opens algorithm control tab - some bug fixes - more examples --- Release notes SplitsTree6 V0_0_13-alpha (Tue, 14 Jun 2022): --- - fixed problem that breadcrumbs did not update - added context menu to breadcrumbs to allow direct access to algorithms - fixed other bugs --- Release notes SplitsTree6 V0_0_12-alpha (Mon, 30 May 2022): --- - fixed problems in tree rerooting algorithms --- Release notes SplitsTree6 V0_0_11-alpha (Mon, 30 May 2022): --- - fixed problems in tree rerooting algorithms --- Release notes SplitsTree6 V0_0_10-alpha (Sun, 29 May 2022): --- - fixed bug that prevented pie chart from appearing in saved haplotype networks. - fixed bug that caused algorithm selection items to not be updated correctly - added examples directory --- Release notes SplitsTree6 V0_0_9-alpha (Wed, 25 May 2022): --- - improved algorithm for guessing sequence type when importing an alignment - update alignment when sites or taxa disabled --- Release notes SplitsTree6 V0_0_8-alpha (Wed, 25 May 2022): --- - Alignment view is now computed in separate thread. - Minor bug fixes - Broken: Embedded images from URLs are not shown --- Release notes SplitsTree6 V0_0_7-alpha (Mon, 23 May 2022): --- - selecting edges: double click selects subtree, option-double click selects other subtree - trees how support edge selection - tree view allows edges to be styled (width and color), and changes are saved to document - selection of edges synchronized across splits networks and tree views in same window --- Release notes SplitsTree6 V0_0_6-alpha (Fri, 20 May 2022): --- - tries to remember where windows were previously opened - splits slider can how be selected in menu --- Release notes SplitsTree6 V0_0_5-alpha (Fri, 20 May 2022): --- - fixed bugs related to selection - added presentation mode - made splits network (rather than outline) default for splits network viewer --- Release notes SplitsTree6 V0_0_4-alpha (Thu, 19 May 2022): --- added PCoA and tSNE to Networks menu - bug fixes --- Release notes SplitsTree6 V0_0_3-alpha (Tue, 17 May 2022): --- CRITICAL BUG FIXES - bugs in neighbor net fixed - added splits slider - some other new features - bug fixes --- Release notes SplitsTree6 V0_0_2-alpha (Wed, 11 May 2022): --- - Cleaned up Neighbor-net options - fixed internal bug that caused problems opening files that used old neighbor-net options - bug fixes --- Release notes SplitsTree6 V0_0_1-alpha (Tue, 10 May 2022): --- - fixed bug that caused some files to fail --- Release notes SplitsTree6 V0_0_0-alpha (Tue, 10 May 2022): --- - Very first alpha release. - Alpha means: : expect many bugs, missing features and future changes