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19/03/18 -*- Version 2.4.0 -*-
19/02/18 Julien Dutheil
* Bug fixed in bppPopStats: dN and dS were inverted!
10/12/17 -*- Version 2.3.2 -*-
06/11/17 Julien Dutheil
* Added estimation of kappa to bppPopStats + bugs fixed
06/06/17 -*- Version 2.3.1 -*-
10/05/17 -*- Version 2.3.0 -*-
21/12/16 Julien Dutheil
* BppPhySamp migrated to its own package.
17/12/16 Julien Dutheil
* Improved bppPopStats, outgroup analyses, MK table and output to file.
06/10/16 Julien Dutheil
* bppSeqGen now takes Hudson's MS ARG files as input.
* new input.tree.scale option to adjust branch lengths.
22/05/16 Julien Dutheil
* bpppopstats now computes codon statistics per site (e.g. PiN, PiS)
* Added example for bpppopstats.
29/06/15 Julien Dutheil
* New program bppPopStats
28/01/15 Julien Dutheil
* PhySamp now outputs the correct tree!
25/11/14 Julien Dutheil
* bppalnscore output contiguous segments in mase selection.
* bppalnscore site selection works with codon alphabets.
24/11/14 Julien Dutheil
* bppSeqMan can now read alignments and perform site selection priori to any analysis.
28/09/14 -*- Version 2.2.0 -*-
16/09/14 Julien Dutheil
* bppSeqGen supports generic characters as ancestral states in info file (bug #87).
12/08/14 Julien Dutheil
* bppSeqGen supports simulation under Markov-Modulated models.
06/06/14 Julien Dutheil
* bppPhySamp now ouput trees as well.
17/04/14 Julien Dutheil
* bppSeqMan: Translate uses global genetic_code argument instead of local 'code' argument.
* All programs use the --seed argument to set random seed for reproduceable results.
08/03/13 -*- Version 0.8.0 -*-
22/01/13 Julien Dutheil
* Compiles with -Wconversion
14/01/13 Mathieu Groussin
* Added COaLA model for proteins in bppML and bppSeqGen.
23/11/12 Laurent Guéguen
* New bppMixedLikelihood program
08/02/12 -*- Version 0.7.0 -*-
21/12/11 Julien Dutheil
* New bppAlnScore program
* Improved bppSeqMan: protein translation now works + more stop codons removal options.
17/06/11 Julien Dutheil
* Improved bppancestor, also allows to compute frequencies for leaves.
11/06/11 -*- Version 0.6.2 -*-
* Small bug fixed + new packages.
03/06/10 -*- Version 0.6.0 -*-
* Compatibility with Bio++ 2.0.0.
03/06/10 Julien Dutheil
* New method in bppPhySamp + new, faster, implementation.
25/03/10 -*- Version 0.5.0 -*-
22/08/09 Julien Dutheil
* Added CMake configuration files, with twick for building the manual (assumes
texinfo is installed).
22/07/09 Julien Dutheil
* Added program bppTreeDraw.
30/06/09 Julien Dutheil
* BppAncestor: now output expected ancestral states frequencies.
* BppAncestor: new method to compute EB estimates of ancestral states frequencies.
10/06/09 -*- Version 0.4.0 -*-
22/05/09 Julien Dutheil
* Keyval syntax for sequence format description.
* Documentation and example update.
* SeqMan now uses the SequenceApplicationTools method.
15/05/09 Julien Dutheil
* Compatibility update with the libs, new keyval syntax for model
specification.
* Documentation up to date.
02/02/09 Julien Dutheil
* bppConsense now outputs the number of leaves of the input tree.
* New progress bar in bppConsense.
08/01/09 Julien Dutheil
* Added texinfo documentation.
* More bootstrap options in BppDist (the same as in BppML).
25/09/08 -*- Version 0.3.1 -*-
07/12/08 Bastien Boussau & Julien Dutheil
* Bug removed in non-homogeneous models with covarions.
09/10/08 Julien Dutheil
* New action 'invert' in bppSeqMan.
25/09/08 -*- Version 0.3.0 -*-
20/09/08 Julien Dutheil
* New program bppAncestor to reconstruct acestral states and rates.
* New +F models from PhylLib.
02/07/08 Laurent Guegen
* Bug fixed in bppML: frequencies can be computed from the data with
non-homogeneous models.
19/06/08 Julien Dutheil
* Shell variables are now 'global' in option files.
24/04/08 -*- Version 0.2.3 -*-
* This version requires the CVS version of Bio++ to be built.
03/03/08 Julien Dutheil
* Bug fixed in keep_complete method of BppSeqMan.
27/03/08 Julien Dutheil
* Bug fixed when printing parameters of non-homogeneous models in bppML.
22/01/08 -*- Version 0.2.2 -*-
28/02/08 Celine Scronavacca
* Bug fixed in ReRoot.
22/01/08 -*- Version 0.2.1 -*-
06/02/08 Celine Scornavacca
* Bug fixed in ReRoot + correction of version number in bppSeqGen.
22/01/08 -*- Version 0.2.0 -*-
13/01/08 Julien Dutheil
* More options in bppml: possibility to chose between simple and double
recursion and data compression method.
* Simple recursion method improved.
11/01/08 Julien Dutheil
* Compatibility update
* bppML now output more handy parameter values.
31/12/07 Julien Dutheil
* New program Phylo Sampler.
07/11/07 Julien Dutheil
* Compatibility update with Bio++ cvs.
* Bug fixed in BppSeqGen.
* BppSeqGen can now simulate datas from a set of trees (ancestral
recombination graph).
25/10/07 Julien Dutheil
* Several bug fixed in BppML and BppSeqGen with non-homogeneous models.
* Examples updated + new example option files for non-homogeneous models.
05/10/07 Bastien Boussau & Julien Dutheil
* Non-homogenous sequence simulation in BppSeqGen.
* Model options in files have changed to suit the non-homogeneous case.
The covarion option now is fully part of the model options, following the
new syntax 'model=modelname+covarionname', eg 'T92+G2001'.
03/10/07 Julien Dutheil
* New program Bio++ Sequence Manipulator
21/09/07 Julien Dutheil
* Bug fixed in BppDist: branch length are indeed not estimated when parameters
to ignore contains "BrLen".
* Stop condition when using iterations is now based on topological distance
instead of likelihood comparisons (phyllib).
* New option optimization.topology_nni.method = [fast|better|phyml]
17/06/07 -*- Version 0.1.0 -*-
16/07/06 Julien Dutheil
* New option bootstrap.verbose for bppML.
* Bug fixed in bootstrap computation.
06/06/06 Julien Dutheil
* New program bppConsense.
05/05/07 Julien Dutheil
* First alpha release of bppsuite.
-*- Old bppML ChangeLog -*-
23/04/07 Julien Dutheil
- Optimization with a global clock.
- Possibility to set branch lengths before ML optimization, with different
methods.
25/01/07 Julien Dutheil
* Version 1.0.0
- Topology search for ML
- User input tree may be random, nj or bionj.
- Possibility to make a parsimony search before ML estimation.
28/08/06 Julien Dutheil
* Version 0.2.0
- Covarion models
- New optimization methods.
30/05/06 Julien Dutheil
* option --enable-static in configure.
19/04/06 Julien Dutheil
* Version 0.1.2
* Update for library compatibility
* Check for 0 branch lengths leading to 0 likelihood before optimization.
* New output.estimates options to get the final parameter values after optimization.
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