PAL: Phylogenetic Analysis Library
This is the place where the current version of PAL (as found in the CVS repository) should
appear about once every week or two. Be warned that not everything might not work (but it should), and that
your code may be broken if it relies on previous APIs. The javadoc pages are not included in the file. And sorry about it
being a zip with windows line endings.
The current release version is 1.5.1 ( for previous versions click here)
Download the Source, API Docs, or
a precompiled jar
- - A bit makeshift - lots of legacy code to deal with still, that's why it's just 1.5.1
- Substatial class rearrangement.
- Nexus alignment reading code (Alex Moore)
- Parially complete new maximum likelihood framework (will do very complex models - eventually).
- New Substitution Models and framework.
- New parameterized framework.
- New sample information framework.
- Temporal changes in substitution model.
- Probably a whole lot of otherthings...
To get email announcements on new updates send an email to:firstname.lastname@example.org
- 15 June 2003 First pre release
- 22 July 2003 First update
- 7 October 2003 Second update, tree rooting enhanced, tool classes moved in. Release 1.5 comming soon with fast and powerful ML tree searching!
- 20 October 2003 Third update, Yang Codon Models fixed, new sUPGMA code, ML Unrooted tree search draft. New algorithmics package. Release 1.5 comming very soon!
- 5 December 2003 Fourth update, little things (like new LeafCalculator, caching, for ML stuff ), Substitution Model changed and in a slighty hacky form (can't redo until after 1.5). New build files thanks to Bruno Afonso, and Thomas Keane. Bug fixes. Version 1.5 for Christmas.
- 16 January 2004 Version 1.5 alpha available. New Tool methods, new classes LikelihoodTool, LikelihoodOptimizer. RobinsonFolds code still faulty. Corrected make file thanks to Thomas Keane.
- 21 May 2004 A quite new update. Quite a few new stuff, all a bit rough. Some nasty bugs fixed. No bug fixes from other people as I haven't included them yet (will soon!)
- 2 November 2004 Version 1.5.1 available
Current CVS(2 November 2004): Download Source
Disclaimer: The authors accept no liability for damages caused by the Current CVS version of PAL.