29/03/11 -*- Version 1.4.1 -*-

21/07/11 Julien Dutheil
* Bug fixed in candidates groups analysis.

29/03/11 -*- Version 1.4.0 -*-

24/11/10 Julien Dutheil
* Debugged Z-score p-value computation.
* Added example directory with simple cases.
* TODO: add built-in p-value computation for CoMap pair test.

19/11/10 Julien Dutheil
* Added new Program Mica, and started to implement efficient pvalue computation.

24/11/09 Julien Dutheil
* Added new MI statistic
* New substitution mapping procedure, base on the probability of observing at
least one jump.

17/09/09 Julien Dutheil
* Switched to CMake building system.
* Compat update with Bio++ devel version.
* A few warnings removed.

07/07/09 Julien Dutheil
* New sign in Grantham distance, so that it makes more sense to use it with
  the compensation method.

22/04/09 Julien Dutheil
* Code and output file format updated + new pairwise analysis.

21/01/08 -*- Version 1.3.0 -*-

18/01/08 Julien Dutheil
* Bug fixed: sites not analysable now have a statistic and p-value of NA
  in the 'candidate' method.

10/01/08 Julien Dutheil
* Compatibility update with Bio++ (future 1.5 release).
* Added support for non-homogeneous models.

07/11/07 Julien Dutheil
* Compatibility update with Bio++.
* Start implementation of new test when candidate positions are available.

05/08/07 Julien Dutheil
* New R scripts: type II test removed, new FDR computation.
* More detailled simulation files for FR computation.
* Possibility to limit the size of the groups in simulation file: faster and
output file smaller.

19/03/07 -*- Version 1.2.0 -*-

* Compatibility update with Bio++ 1.4.

19/03/07 -*- Version 1.1.0 -*-
* Need the latest CVS version of Bio++
* Update for compatibility with Bio++ 1.3.
* Weighted substitution mapping: possibility to use a weight from AAIndex 1
and 2.
* Compensation test.
* New p-value computation procedure.

29/08/06 -*- Version 1.0.1 -*-

25/08/06 Julien Dutheil
* Update for compatibility with PhylLib 1.2.
* Removed garbage output when simulating.
* New method for detecting compensatory mutations (beta).

26/07/06 Julien Dutheil
* Version 1.0.0 (first public release).
