
2015-04-23	Version 2.1.4
 * Removed as many clang compiler warnings as possible
   => induced minor rounded differences in distances computation, which have no effect on tree inference

2015-02-10	Version 2.1.3
 * Outputted distance matrix may contain 'NA' when distance cannot be computed
 * Harmonized CLI short and long options
 * Harmonized default values for CLI and PHYLIP interface
 * Added FLU model
 * Debugged model assignation for HIVb & HIVw
 * Improved parallel bootstraps status display

2014-10-28	Version 2.1.2
 * Added possibility to compute only distance matrix
 * Removed scoredist routine.
 * Debugged BioNJ NJ UNJ when bootstrapping
 * Debugged long float printf format (printf ("%lf")) not supported by Windows.
 * Added pseudo-counts for stationary probabilities computation for proteins.
 * Detected problem with TBR procedure, removed from available options.

2014-01-27	Version 2.1.1
 * Debugged 'calcTN93' in 'distance.c'.
 * Added RY and F81 models for DNA.
 * Added Poisson (F81-like), HIVb and HIVw models for proteins.

2013-03-17	Version 2.1.0
 * Implemented parallelized protein distance matrix computation with OpenMP.
 * Implemented parallelized bootstraps computation with OpenMP.
 * Debugged bootstraps procedure.
   Adjust 'ijFilter' in 'distance.c' to work with bootstraps.
   Create a model structure for each thread for protein distances.
 * Removed  'CompDist.c' 'CompDist.h' 'FastDist.c' 'FastDist.h'.
 * Added 'T' option for command line to set the number of threads.

2012-11-12	Version 2.09
 * Debugged 'calcF84' in 'distance.c'.
   Gamma law was not used when asked for.
 * Debugged 'Opt_Dist_F' in 'p_optimize.c'.
   Fix Brent initialization incorrect value.
 * Implemented parallelized DNA distance matrix computation with OpenMP.
 * Removed compilation warnings.
 * Debugged 'loadMatrix' in 'inputs.c'.
   Check input matrix contains number of taxa on first line.
 * Debugged 'bionj' in 'BIONJ.c'.
   Fix output string length problem when branch length has more than 3 digit
   before comma.

2011-05-28	Version 2.08
 * Allow gamma law for distance computation for DNA and proteins.
   Gamma parameter (alpha) is set to 1.
 * Debugged 'fastme.c'.
   Rewind to begin of newick string when using input tree and bootstraps.
 * Added required memory space estimation for NNI/SPR/TBR.
 * Harmonized CLI and PHYLIP interface behaviour for NNI/SPR/TBR.
 * Added JC69 model.
 * Updated ML distance computation for protein in 'p_lk.c'.
   Do not compute distance when sequences are identical.
 * Removed fastdist implementation for DNA distance computation.
   (FastDist.c FastDist.h CompDist.c CompDist.h)
   Distances are computed using analytic formulae.
 * Debugged 'makeDistMatrix' and 'ijFilter' in 'distance.c'.
   Sequence length was not decreased when doing pairwise gap removal.
 * Debugged 'Read_One_Line_Seq' in 'p_utils.c'.
 * Removed several compilation warnings:
   - Ignoring return value of 'scanf', ...
   - No format string for 'printf', ...
 * Introduced 3 verbose levels.
 * Harmonized utilities functions usage through the code:
   - mCalloc
   - Message
   - Warning
   - Exit
 * Removed memory leaks.

2008-10-29	Version 2.07
 * Harmonized models global constants and corresponding functions names.
 * Set default model to F84 for nucleotides and to LG for amino-acids.
 * Corected option argument error when choosing SCOREDIST model.
 * Added 'a' option for command line to append results to output files.

2008-07-18	Version 2.06
 * Added 'p_bootstrap.c' to finalize bootstraps.
   (heavily borrowed from PhyML).
 * Added the boostrap trees output file.
 * Removed 'print.c' and 'print.h'.

2008-03-10	Version 2.05
 * Removed 'interface_free.c'.
 * Added 'p_eigen.c' 'p_lk.c' 'p_models.c' 'p_optimiz.c' 'p_utils.c'.
   Integrate distance computation from protein alignment
   (heavily borrowed from PhyML).
 * Replaced discrete gamma law by continous gamma law.

2007-12-12	Version 2.04
 * Debugged newick.c.
 * Added 'BIONJ.c' and 'MVR.c' to implement NJ, BIONJ and UNJ algorithms.
 * Added 'interface_options.c' 'interface_utilities.c' 'interface_free.c'.
   To manage:
   - PHYLIP like interface
   - Command line interface
   - Man like usage
 * Added an extra information file output (_stat.txt).
 * Formatted the standard and verbose output.
 * General code structure cleaned, generalization of header files.
 * Security issue:
   Replaced unsafety functions (strcpy strcmp sprintf)
   by their safety equivalent functions (strncpy strncmp snprintf)
   to avoid buffer overflow.

2007-09-27	Version 2.03
 * Debugged 'TBR.c'.
 * Added 'CompDist.c' 'FastDist.c'.

2007-09-21
 * Written TBR routine.

2007-07-19	Version 2.02
 * SPR routine is rewritten, fixed, and a bit faster.

2007-07-11	Version 2.01
 * Added gamma rate variation.
 * Changed gap filter to be pairwise by default.
 * Reduced node labels to nine characters at maximum.
 * Added capability of sequence input to ignore space characters in
   sequence.

2005-09-01	Version 2.0
 * New release.

2005-08-01
 * Finished distance formulae.
 * Added NJ routine for building initial tree.
 * Added *.mat score matrices for scoredist routine.
 * Bootstrapped functionality verified.
 * Minor change to tree building:
   Nodes in set 'species' are not used in tree.
   This change is to allow bootstrapping to repeatedly
   build multiple trees on the same set of nodes.

2005-07-13	Version 1.5.1
 * Added more protein formulae.

2004-07-12	Version 1.5
 * Added SPR functionality.

2004-11-17	Version 1.4.1 
 * Added ability to handle gapped sequences.

2004-10-6	Version 1.4
 * Added distance estimation capability from sequence data.

2003-02-28	Version 1.3
 * Expanded search of bNNI to retest all edges, rather than only edges
   adjacent to changed edge.

2002-11-19	Version 1.2.1
 * Fixed parts of newick.c to make it preserve the exact order of the
   input topology.

2002-10-01	Version 1.2
 * Added ability to simply assign OLS or balanced weights on an input
   topology, without doing any NNIs.

2002-09-01	Version 1.1.2
 * Removed bug in main program in print statement called only in verbose
   mode.

2002-08-26	Version 1.1.1
 * Removed bug in 'NNI.c'.

2002-06-06	Version 1.1
 * Added ability to handled data sets with more than one matrix in an
   input file, as well as the ability to handle more than one input tree.

