File: General Notes.txt

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This file is intended as a reference for all important changes made to the PAL source code.
===========================================================================================

11 Oct 2002
	- Removed AminoAcidAlignment as it's redundant. (See pal.alignment.DataTranslator for an Alternative)
	- Removed SimpleAlignment constructors that create null datatype - caused t0o many hard to find bugs (MG) (if datatype not know just pass null - but that's a bad idea)

28 Oct 2002 (Accidentally clicked commit when I wasn't supposed too...)
	- Changed MinimiserMonitor slightly...

21 March 2003 Lots of changes
	- DataType includes gap stuff, DataTypeUtils moved to DataType.Utils
	- Updated web page (begun migration to www.cebl.auckland.ac.nz/pal-project

.....
	- DatedTipsTree removed - use MutationRateModelTree

23 June 2003 Lots of changes
	- Added AlignmentReceiver, changed AlignmentReaders to read multiple phylip/clustal
		alignments from one file
1 July 2003
	- Added setResidueFont() to TreePainter stuff
14 October 2003
	- Major addition of new Unrooted tree search tool. Includes the addition of pal.algorithmics, and pal.treesearch, and changes to pal.eval.
	- Also added pal.mep.DeltaModel which is used by new tools to be added soon
18 October 2003
	- Added sUPGMA code though no signs of how to use it yet (will add tool class later...)
	- Yang Codon Models fixed
5 December 2003
	- Lots of fixes
	- New Ant make file (Bruno Afonso)
	- New windows make batch file (Thomas Keane)

2 November 2004
	- Bug fixes
	- New Nexus reading code (Alex Moore)
	- Partially complete new likelihood framework
	- New parameterized interface
	- New substitution models 
	- Temporal changes in substitution model 
	- New sample information interface