28

Release History:

21-11-2005 - Ver 0.28
  - Minor mods to BAMBE's source to make it compatible with GCC4 compilers.
    Thanks to Sylvain Foret.
    
31-05-2005 - Ver 0.27
  - Edited and recompiled BAMBE with optimizations for Windows, so it's now
    about 30% faster on that platform.
  - New installers created using install4j rather than InstallAnywhere.

09-05-2005 - Ver 0.26
  - Changed the server used by the updater facility.

14-04-2005 - Ver 0.25
  - Implemented "Pruned PDM" as described in "Detecting interspecific
    recombination with a pruned probabilistic divergence measure" published in
    Bioinformatics (2005). Unix/Linux users will need to compile TreeDist in the
    binaries directory which this new method now relies on.
  - Fixed a bug in PDM that was incorrectly calculating the threshold line when
    bootstrapping was used.
    
05-04-2005 - Ver 0.24
  - The HMM (BARCE) analysis method has had an improved sampling scheme
    developed for it by Adriano Werhli, which dramatically reduces the
    computational costs when running it. You should also restore the default
    settings for HMM before running. UNIX/Linux users must also recompile BARCE
    for the changes to take effect.
  - Fixed some minor incompatibilities with the input files sent to BAMBE.

01-12-2004 - Ver 0.23
  - Fixed a bug that was blocking editing of (existing) partitions in Java 1.5
    on xwindows systems.
  - Fixed a bug in the Find Sequence dialog that affects how the display is
    updated if the sequence was found.
  - Fixed a (potential) bug that could have multiple users of TOPALi on Unix or
    Linux machines all accessing the same temp disk space.
  - Other misc bug fixes that I forgot to document at the time!

24-05-2004 - Ver 0.22
  - Fixed some errors in the keyboard shortcuts of the Alignment menu.
  - Added a (requested) option to move a group of selected sequences to the top
    of the alignment. Also added in the ability to move (up or down) more than
    one sequence at a time.
  - Disabled the ability to bootstrap trees with the bayesian tree creation
    method as it is not needed.
  - When importing protein alignments, TOPALi will now prompt for a matching DNA
    alignment file (3x the length of the protein file) in order to convert the
    protein alignment to DNA.

26-03-2004 - Ver 0.21
  - Added the ability to generate trees with bootstrap values. The user can
    select any number of bootstrap iterations to compute, from 10 to 10,000.
  - Fixed a bug when using DSS/Fitch that affected sequences with badly formed
    names.
  - Improvements to the code for printing trees. Hopefully larger trees should
    print properly over multiple pages now.

02-03-2004 - Ver 0.20
  - Added the ability to launch TOPALi via associating .top files with the
    InstallAnywhere launcher (TOPALi.exe on Windows). Two things to note here:
    you have to set up this association yourself, and you'll need to do a fresh
    install of TOPALi using the latest version available on the web - running
    TOPALi's built-in web update will not install this feature for versions
    prior to 0.20.
  - Adjusted partitioning code so that partitions will go from x1 to x2 and x2+1
    to x3 rather than from x2 to x3.

28-01-2004 - Ver 0.19
  - Modified the Partitions dialog so that its partitions are always displayed
    in numerical order (rather than order of creation).
  - Further additions and modifications to the user-manual.

18-12-2003 - Ver 0.18
  - TOPALi is now Mac OS X compatible (tested on Panther only).
  - Fixed a bug related to running BAMBE on Windows 95/98.
  - Better default font selected for running on Linux.
  - Adjusted Mosaic Panel sequence divergence threshold increments to 0.005 up
    from 0.01.
  - New colour-gradient titles added to certain dialog boxes to make them look a
    bit less plain.
  - Additional options added to NEXUS output to allow the files to be used with
    SPLITSTREE and PAUP*. Summary info also added to these files if the entire
    alignment is being saved.

03-11-2003 - Ver 0.17
  - Find Sequence option added to the Alignment menu.

28-11-2003 - Ver 0.16
  - Phylogenetic informative site information added to Summary Info dialog.
  - Topology Defining Sites (TDS) algortihm added to populate topology structure
    in the HMM settings dialog.
  - New source code for BARCE added giving full linux compatibility.

23-10-2003 - Ver 0.15
  Added support for MSF formatted alignments.

02-09-2003 - Ver 0.14

18-08-2003 - Ver 0.13

15-08-2003 - Ver 0.12

12-08-2003 - Ver 0.11

07-08-2003 - Ver 0.10

04-08-2003 - Ver 0.09

16-07-2003 - Ver 0.08

01-07-2003 - Ver 0.07

30-05-2003 - Ver 0.06

21-05-2003 - Ver 0.05

12-05-2003 - Ver 0.04

07-05-2003 - Ver 0.03

02-05-2003 - Ver 0.02

30-04-2003 - Ver 0.01