--- Release notes Dendroscope V3_8_10 (Wed, 6 Sep 2023): --- - fixed a bug that caused level-k and galled network to fail --- Release notes Dendroscope V3_8_9 (Wed, 23 Aug 2023): --- - fixed a bug that caused problems when parsing a Newick file with confidence values saved as edge comments --- Release notes Dendroscope V3_8_8 (Thu, 6 Apr 2023): --- - really? fixed *null color* exception that sometimes occurs --- Release notes Dendroscope V3_8_7 (Sat, 25 Mar 2023): --- - fixed *null color* exception that sometimes occurs --- Release notes Dendroscope V3_8_6 (Fri, 24 Mar 2023): --- - updated installer --- Release notes Dendroscope V3_8_5 (Wed, 7 Dec 2022): --- - fixed bug that prevented parsing of some rooted networks in extended Newick format - fixed update URL --- Release notes Dendroscope V3_8_4 (Tue, 30 Aug 2022): --- fixed bug that prevented galled networks from working --- Release notes Dendroscope V3_8_3 (Mon, 30 May 2022): --- - fixed bug that prevented use of Cluster Network Consensus --- Release notes Dendroscope V3_8_2 (Wed, 9 Mar 2022): --- - added command-line option to turn off *confirm quit* dialog --- Release notes Dendroscope V3_8_1 (Sat, 12 Feb 2022): --- - supports MacOS M1 chip --- Release notes Dendroscope V3_8_0 (Fri, 11 Feb 2022): --- - supports MacOS M1 chip (This might not work, if not, there will be another update soon) - minor bug fixes --- Release notes Dendroscope V3_7_6 (Wed, 25 Aug 2021): --- - fixed a bug in Extract Induced Network - Fixed a bug in Selected subnetwork - Fixed a bug in scale horizontally --- Release notes Dendroscope V3_7_5 (Fri, 9 Apr 2021): --- - fixed some issues with nexus parsing --- Release notes Dendroscope V3_7_4 (Thu, 28 Jan 2021): --- - Fixed bugs related to nexml output and input --- Release notes Dendroscope V3_7_3 (Fri, 27 Nov 2020): --- - Fixed bug in rerooting function --- Release notes Dendroscope /V3_7_2 (Mon, 17 Feb 2020): --- - fixed bug that prevented scrolling of tree or network in some situations --- Release notes Dendroscope /V3_7_1 (Sat, 15 Feb 2020): --- - Fixed newly introduced bugs that broke many of the drawing algorithms --- Release notes Dendroscope /V3_7_0 (Tue, 11 Feb 2020): --- - notarized MacOS installer to be compatible with latest Catalina OS - minor bug fixes --- Release notes Dendroscope /V3_3_2: --- - removed defunct registration code --- Release notes Dendroscope /V3_3_1: --- - fixed fatal error that prevented saving in nexml format --- Release notes Dendroscope /V3_3_0: --- - First open source edition of Dendroscope under GPL license - Source files available here: http://danielhuson.github.io/dendroscope3/ --- Release notes Dendroscope /V3_2_10: --- - Rewrote command-line options interface - Fixed problems related to running some algorithms in command-line mode --- Release notes Dendroscope /V3_2_9: --- - Added command (in advanced algorithms) that lists the distance to the root for all selected taxa --- Release notes Dendroscope /V3_2_8: --- - Fixed bug that prevented help command from working --- Release notes Dendroscope /V3_2_7: --- Modified Newick parser so as to allow spaces and punctuation characters to appear in labels, if surrounded by single quotes, so as to establish compatibility with Geneious --- Release notes Dendroscope /V3_2_6: --- - Fixed a bug that prevented reopening of some trees saved in nexml format --- Release notes Dendroscope /V3_2_5: --- - Toolbar radio buttons are now shown as pressed - a number of bug fixes --- Release notes Dendroscope /V3_2_4: --- - Fixed bug the prevented regular expressions from wokring correctly in Find --- Release notes Dendroscope /V3_2_3: --- Added primodial consensus --- Release notes Dendroscope /V3_2_2: --- Some minor bug fixes --- Release notes Dendroscope /V3_2_1: --- Added set font command to command-line parser Updated version of Cass algorithm for computing level-k networks --- Release notes Dendroscope /V3_2_0: --- - Removed Find/Replace dialog and replaced it by a new Find and Find/Replace tool bar. - Fixed bug in Hybrid number code that sometimes caused hybrid number to be incorrect on multifurcating data (the refinement step in the main loop of the algorithm was missing in the hybrid number code, but not in the hybrid network code) - Fixed bug in hybrid network code that caused the number of networks computed to differ depending on the order of the input networks (caused by MAAF reduction being called after reattachment of dead taxa, should be before) - Paper on Dendroscope3 submitted. - Some minor corrections in manual. --- Release notes Dendroscope /V3_1_0: --- - Reorganized menus and placed many advanced features that are probably not of great general interest into a number of "advanced" submenus - Added new algorithms for computing hybridization networks for rooted trees that are not necessarily binary and do not necessarily contain the same taxa, to coincide with the submission of a paper on the topic. - Number of minor bug fixes - Updated user manual --- Release notes Dendroscope /V3_0_14beta: --- - Modified List Selected menu item so that taxa are listed in the order that they appear in (not alphabetical order) - Added a new method for multi-labeled trees that makes them single-labeled by contracting all edges on the path between two different instances of the same label --- Release notes Dendroscope /V3_0_13beta: --- - added alpha value to format dialog - fixed fit-to-panel function so that trees remain visible when panels are resized --- Release notes Dendroscope /V3_0_12beta: --- Fixed error in commands for setting colors. Extended syntax for specifying colors in command-line mode: Now can specify X11 name of color, or single hex number, or r g b or r g b alpha (the latter specification allowing transparency) --- Release notes Dendroscope /V3_0_10beta: --- - Added configuration of heap memory to installation script - Fixed bugs in "delete taxa" and "edit labels" that prevented these changes from being written back to the underlying data representation (i.e. causing the changes to have no long term effect). - Changed the internal representation of clusters. This should make some methods much faster, but there is also the chance of unwanted side-effects. If you suspect a bug, please let us know. --- Release notes Dendroscope /V3_0_9beta: --- - Fixed bug in hybridization network code that caused the number of networks to be incorrect in some cases --- Release notes Dendroscope /V3_0_9alpha: --- - Fixed bug that prevented export images command from functioning correctly under windows - Fixed minor bug in command line help command - FIxed minor bug in find command - Modified dendro parser so that old files that have a particular bug in them can still be read anyway --- Release notes Dendroscope 3_0_0alpha: --- All new version of Dendroscope. Replaces Dendroscope2. Main new features include the possiblity to view many trees simutaneously and a number of new methods for computing rooted networks. Also features a tanglegram view that works both on trees and networks. The tanglegram view does not require that the trees or networks are bifurcating, or that they are even on the same set of taxa.