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29/04/18 -*- Version 1.3.0 -*-
13/04/18 Julien Dutheil
* Error output when not enough ingroup sequences in DiversityStatistics and SiteFrequencySpectrum
09/03/18 Julien Dutheil
* Logfile can now be disabled
* Merge filter can now rename chimeric contigs to avoid long concatenated names.
21/01/18 Julien Dutheil
* Added OrderFilter.
16/12/17 Julien Dutheil
* Added OutputAsTable filter
* Improved LiftOver
18/05/17 -*- Version 1.2.0 -*-
13/04/17 Julien Dutheil
* Possibility to allow for dots in maf alignments (treated as gaps)
* VCF output can included non-variable sites (experimental)
* Added support for tree-based filtering
04/06/16 Julien Dutheil
* Alignment filters now accept frequencies as maximum amount of gaps.
23/06/16 Julien Dutheil
* Possibility to count characters for a selection of species only.
18/06/16 Julien Dutheil
* Added call to external tree reconstruction program.
26/04/16 Julien Dutheil
* Added distance matrix output.
* Added RemoveEmptySequences filter.
09/02/16 Julien Dutheil
* Features in BedGraph format are now supported.
* New LiftOver filter.
18/12/15 Julien Dutheil
* SequenceStatistics can now write in compressed file.
10/12/15 Julien Dutheil
* Added PLINK export filter.
22/11/15 Julien Dutheil
* Fixed bug in FeatureFilter in case two features are exactly consecutive.
20/10/15 Julien Dutheil
* Added Tajima's pi to diversity statistics.
13/01/15 Julien Dutheil
* More options for OutputAlignments (output file names).
09/01/15 Julien Dutheil
* Add formatting options (sequence names) for trees and distance matrices.
* ML parameter estimation outputs parameter names in terminal.
26/09/14 -*- Version 1.1.0 -*-
05/04/14 Julien Dutheil
* Added ML model fit (stationary and non-stationary).
25/07/13 -*- Version 1.0.0 -*-
15/01/2010 Julien Dutheil
* Initial version.
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