Releases will be numbered with the following semantic versioning format:

<major>.<minor>.<patch>

And constructed with the following guidelines:

* Breaking backward compatibility bumps the major (and resets the minor 
  and patch)
* New additions without breaking backward compatibility bumps the minor 
  (and resets the patch)
* Bug fixes and misc changes bumps the patch

February 2014: PIBUSS version 1.3.5
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* Sequences in the alignment are now in the tree traversal order
* Added MG94 codon model

April 2014: PIBUSS version 1.3.6
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* Option to output ancestral sequences
* Starting sequence is now called root sequence to avoid confusion

September 2014: PIBUSS version 1.3.7
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* Fixed bug that cause non-randomized draws from relaxed clock models 
* XML generator adds "randomizeRates=true" attribute to DiscretizedBranchRates elements
* Added additional parameter to the NewickParser which allows the user to use node heights without specifying dates for taxa.
* Sensible starting values for UCLD clock

PIBUSS version 1.3.8 release candidate
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* Parameters of the relaxed lognormal clock are now on the log scale by default and can be changed in XML or in CLI (-lrcParametersInRealSpace true|false). 
  GUI is hardcoded to true.
* Tool-tip for ucld mean and stdev fields that says these parameters are in the real space
* XML parser checks siteCounts per partition; previously this behaviour could throw an exception if using rootSequences with multiple partitions
* Fixed a bug in SiteRate model XML generation; when using multiple partitions alpha parameter was not raised by suffix
* Fixed a labelling of the Gamma Site Rate model in the appropriate editor