Updated documentation

Author: muffato

README.md

@@ -11,8 +11,19 @@ The main new features are:
 * new "T" node-tag in the NHX output: a bit-field listing the input trees that support the node. This is populated by the _mmerge_ algorithm
 * new `-Z` argument to `treebest best`, to redefine the PhyML variable `MIN_DIFF_LK`. It prevents PhyML from crashing during its computation
 * new `-s` argument to `treebest sdi`, to allow a user-defined species tree. This change is from [Albert Vilella](https://sites.google.com/site/avilella/)
+* new `-X` argument to `treebest best`, to give a higher weight to the likelihood that comes from the reconciliation with the species tree (default 1)
+* Species-Intersection Scores are now reported as floating-point values (with 2 decimals)
 
 Other changes include:
 * bugfixes / tweaks when processing the filtered alignments (TreeBeST includes a Clustal-score-based MSA-filtering step)
 * bugfixes / tweaks when merging the trees
 * using `double` instead of `float` for floating-point values
+
+## Branches and tags
+
+There is a single branch where all the development goes. The version number stated in the source code (1.9.2) is not maintained.
+
+Tags are used to point at specific versions:
+* lh3 (currently 2a4fe3): when Heng Li handed-over the code to Ensembl Compara
+* albert (currently 5e20c4): changes made by [Albert Vilella](https://sites.google.com/site/avilella/)
+* ensembl\_production (currently 24637d): the version currently used for Ensembl's production