== 0.9.0, released 2009-2-13

* Added --heatmap option for heat map generation from substitution tables
* Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
* Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
* Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
* Added --heatmap-value option to print values in the cells of heat maps
* Renamed --noround option to --noroundoff
* 'simple_memoize' RubyGem package is no longer required

== 0.0.5, released 2009-1-23

* Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
* Added --augosigma option to avoid excessive influence of background frequencies
* Added --noround option was added to get original log odds ratios
* Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
* Fixed a bug in p2 probability calculation of the partial smoothing procedure
* Fixed a bug in total probability/log odds ratio calculation
* Changed default verbosity from ERROR to WARN
* Refactored codes to be more human readable and DRY

== 0.0.4, released 2008-12-15

* Fixed a bug to generated log-odds ratio matrices with --nosmooth option
* Copes with no observations or mutations

== 0.0.3 2008-12-09

* Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
* Fixed a bug to make masking works for target amino acid, too

== 0.0.2, released 2008-11-13

* Supports user provided constrained environment features are properly handled

== 0.0.1, released 2008-11-07

* Initial release