1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
|
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
|