v1.22 : Bugfix related to top placement scores

* Fixed the kth selection algorithm that sometimes missed top results

v1.21 : Support for RAxML-ng ancestral reconstruction

+ support for ancestral reconstruction computed by RAxML-ng (~10x faster than phyml)
+ 'paml', 'phyml' and 'raxml-ng' binaries can be called via '-b/--arbinary'
+ option '--threads' allow to use several CPUs in RAxML-ng reconstructions
+ project configuration migration from Netbeans to IntelliJ IDEA
+ external library now managed via MAVEN (where possible)
- removed dependancies to libraries used only in outdated debugging functions
* minor logging changes

v1.12 : Improved accuracy and phyml 3.3.20190909 support

* bugfix in phylo-kmer generation: DB build is slower but placement is now more accurate !
* default omega set to 1.5, for improved speed/accuracy balance.
* compatibility with phyml v3.3.20190909, it is highly recommended to update as it corrects a critical bug in ancestal reconstruction.
* minor changes related to verbosity
+ add stub.sh to rapidly build a standalone binary (no call to "java -jar"), instructions in README

v1.11 : HOTFIX (29/05/2019) Full support of nucleotides/amino acids ambiguities

* bugfix related to wrong definition of ambiguity X
* bugfix related to lower case ambiguities that were not parsed correctly
  !! This breaks compatibility for DBs built with previous versions. !!

v1.10 : full support for ambiguous states

+ added full support for ambiguities present in the query sequences
  !! This breaks compatibility for DBs built with previous versions. !!
+ ambiguities for nucleotides (R, Y, S, W, K, M, B, D, H, V, N, I, *, .,  !)
+ ambiguities for amino acids  (X, . )
+ phyml version is now explicitely tested before execution to ensure compatibility
- ambiguity support breaks compatibility with previous versions
- you do not anymore to define the states (-s) in placement phase, as this information is now saved in the database.
* ambiguity support will produce slightly different placement scores
* bugfix related to some phantom branch lengths that were incorrect

v1.05 - RAPPAS manuscript revisions

+ some refactoring to simplify the DB code.
- this makes DBs built with v1.05 or later incompatible with previous versions !
+ option to output a jplace with same column order than in pplacer, making the output compatible with guppy
* corrected an important bug introduced in v1.04 where distal and pendant length were flipped in the jplace output

v1.01

First stable version. Made public for review.