GitLab

* fixed tree coloring bugs
* tree branch/node/leafname coloring newick tags: C / BC = red / rgb(255,0,0) / 255.0.0 / #ff000
* global tree settings: custom metadata tag for leaf or node label, node spot size
* node-specific newick tags for overriding global settings: NL= S / GN / NHXtag (node/leaf label) CR=3/4/5... (node spot size)

* Added CORS and JSONP support for serverless cross-origin data import
* Better metadadata parsing from NHX trees (add custom tags via NewickMeta dictionary)
* Custom tree node and branch colors (PhyloXML "color" or NHX "C" and "BC" tags)
* Updated jQuery libraries

* Fixed: No link between tree and alignment if fasta header contains id and description (issue #1)
* Fixed: index.html file as an HTML attribute type (issue #2)
* Fixed: Load tree and msa files from 2 urls at the same time fails (issue #4)
* Fixed issues with tree rendering (branchlength overflow, 0-length branches, name tag positioning, metadata Ensembl links)
* Wasabi server: better handling of corrupt/missing metadata in analysis library

Bug fixes: plugin system, tree lost when saving. Added: "check" attribute to plugin system and Pagan plugin. Delete option in leaf menu with treeless import.

* Alignment position now retained after translation
* Bug fixes
* Changed licence from GPL to AGPL
* Added CITATION, README and LICENCE text files

* NEXUS file import and export (supports "trees", "matrix" and "translate" commands);
* import files without wasabi server (also with URL parameters "url=" or "file= ").
* Leaf color support (with newick tag "[&&NHX:C=color]" or PhyloXML "color" attribute)

Plugin system finished: delivery from plugins folder (+ Pagan relocation), support for positional arguments.

* Bug fixes. This is stable version with no known issues.
* New: plugin system. Pagan support reimplemented using plugin API (new interface, with placement mode).
* Anlaysis library updates: Create and share collections. Path view. Add metadata.
* Save dialog: store coloring/scroll position state
* Option for creating a temporary user account
* Smaller modifications (new "update alignment" notification etc.)

* New library breadcrumb

Added piwik analytics
Interface builder for Wasabi plugin API
Bug fixes

*Drag/drop library item move
*Folder sharing UI

* Library ID tracking moved to indexing (+duplicate check)
* Can create empty library folders
* Can share whole analysis folders (+move/copy/delete) + UI side
* Can copy/move analyses in library
Javascript: bug fixes
* user creation, analysis (auto)save target

* Ready for stand-alone distribution
* Linux desktop shortcut