Version History

PhyDE 0.994
December 2007
  • Complete rewrite of graphics function. Now millions of bases can be displayed.
  • Double-click to edit taxon names
  • Auto-scroll when resizing selection
  • New font sizes "small", "very small", "tiny" to get overview over large alignment stretches
  • Change font size via scroll wheel of mouse
  • Different default colors for amino acids, better reflection of chemical similarity (thanks to Claude dePamphilis for his help with this)
  • New edit operation "insert gaps in others" (shift-space), where gaps are inserted in all sequences but the selected ones (thanks to Claude dePamphilis for suggesting this)
  • Double-click on labels for label editing and deleting
  • New label list to quickly browse labels and go to corresponding alignment position
  • New button to add label (= alt-L)
  • Multiline labels: tooltip text will display multiple lines of text to allow lengthy label entries
  • Character sets are displayed as colored bars above alignment. Multiple lines will be shown for overlapping character sets, depending on which sets are selected for display in the character set editor (CSE). Colors can be set via the character set editor, too.
  • When moving mouse on a column above the alignment, tooltip text displays all character sets the current column belongs to
  • Character set definitions (begin/end) will be auto-adjusted when edit operation affect all lines simultaneously (but also upon the new edit operation “insert gaps in others”).
  • Help browser online and local.
  • Network settings via Edit menu.
  • Auto-check if newer version is available.
  • New plug-in function enhance the plug-in interface (e.g., have the plug-in directly open files in PhyDE or ask PhyDE to export data to file)
PhyDE 0.993
  • Fixed error concerning files without any sequence data.
PhyDE 0.992
  • 0.992: Bug fixes and auto-locate in trace files.
  • Sequence headers. Editor for new header entries in Taxa menu.
  • Smaller file size.
  • Removed Charset-Mode. Instead, charsets are painted over the alignment. Transparency can be set with slider.
  • Files can be dragged into an alignment window to open them (Windows&Mac)
  • View:>Tile alignment windows
  • Removed main application window. Moved its menu entries to alignment window.
  • Labels can be edited
  • New plugin to save header data in text files
  • Scroll to column in View Menu
  • Choices in View Menu
  • Extended File:>File Settings-Dialog
  • Extended plugin interface (for JAVA-Programmers)
PhyDE 0.9.8
  • Completely new handling of Proteins ("Amino-Switches"). Every sequence may contain an arbitrary number of regions which will be displayed as proteins ("Mixed" submode of standard mode)
  • new functions "Set global frame" and "Delete all switches" (Taxa menu). These simplify the input of the switches.
  • Backspace also possible in column 0
  • Errors & Messages window (Help menu in application window)
  • The genetic code selector has moved to File:File Settings
  • Improved FASTA reading.
  • Increased maximal sequence length to 25000000
PhyDE 0.9.7
  • Consensus sequence (Taxon-menu)
  • Length of selection without gaps is displayed in braces
  • "Find taxon name" in "Taxon"-menu
  • PhyDE-Symbol is drop target for opening files.
  • File settings in File-menu: Select data type (amino or nucleotide). Useful when importing from FASTA files. Not to be confused with "Convert to Aminos"!
  • improved import of FASTA files from GenBank
  • Comments etc. are displayed
  • changed "uninf" character set
  • Reactivated "overlap" function. Not yet fully functional.