Download
Main program
| PhyDE0995 |
ZIP compressed JAR file.
Unzip, and then execute with java -jar PhyDE0995.jar
For Java 5.0 or newer |
| PhyDE0995-j2 |
ZIP compressed JAR file.
Unzip, and then execute with java -jar PhyDE0995-j2.jar
For Java 2.0 or newer |
The current version is 0.995 from Jan 17, 2008.
Attention Mac-Users!
- The next version will require Java 5.0 (JRE 1.5).
- The default settings of MacOS X seem to be that the above zip archive is decompressed recursively, and a jar file is also a zip archive. To avoid that, you could use "unzip" in the command-line.
Plugins
| abi2scf |
Converts ABI files to SCF. |
| saveheader |
Write header data of alignment files to text file. |
| SeqState |
Primer design, sequence statistics, and indel coding according to various schemes. |
| PRAP2 | Parsimony- and likelihood ratchet analysis |
Installation: A plugin consists of at least two files: A description (.dsc) file and an executable (.jar).
For installation, unzip the archive and move its contents
into PhyDE's "plugins"-folder in the directory "PhyDE-Data".
System requirements
PhyDE runs on every system with the Java 1.5 Runtime environment (aka Java 5) or newer installed.
What's new in 0.994/5?
0.995:
- arrange windows (Ctrl-U)
- Ctrl-D (view source file) works with more than one sequence
- bug fix in pherograms
0.994:
- Users of version 0.993, please delete the file ~/PhyDE-Data/prefs
- Complete rewrite of graphics function. Now sequences with many 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 functions enhance the plug-in interface
Previous changes in the Version history
How to purchase full version
The JAR file above is a 30-day trial version. After that time, a password is required to
continue using it (and all future releases).
A single student license costs 30€, please read here← for more information.