CHANGELOG

v1.21
- removed dependancies to Guava and Jfreechart, which were related to outdated debug functions

v1.20

+ project configuration migration from Netbeans to IntelliJ IDEA
+ external library now managed via MAVEN (where possible)
+ 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
* minor logging changes

v1.12

* bugfix in phylo-kmer generation: DB build is slower but placement is now more accurate !
* default omega set to 1.5, for more speed/accuracy balance.
* compatibility with phyml up to v3.3.20190909
* minor changes related to verbosity
+ added stub file to build 'rappas' binary and avoid usage "java -jar" prefix, instructions are in README.md

v1.11
* 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. !!

v1.1
+ added full support for nucleotide/amino acids ambiguities.
  !! This major change breaks compatibility for DBs built with previous versions. !!
  !! It will also produce slightly different placement scores. !!
+ phyml version is now explicitely tested before execution to ensure compatibility
+ when a user uses an unrooted tree, he has now to explicitely confirm this choice as root choice may impact accuracy
- you do not anymore to define the states (-s) in placement phase, as this information is now saved in the database.
* bugfix related to some phantom branch lengths that were incorrect

v1.05
+ option to output a jplace with same column order than in pplacer, making the output compatible with guppy
+ some refactoring to simplify the DB code
+ added onlyX1 debug option
* corrected an important bug introduced in v1.04 where distal and pendant length were flipped in the jplace output

v1.04
+ added options to set more easily the model used during AR (options -m,-a,-c)
+ added --arparameters options to pass parameters directly to the AR software (useful for phyML tuning) 
* options -a (alpha) renamed -o (omega) to avoid confusion with Gamma shape parameters

v1.03
+ added UOX amino acids support (option --convertUOX)
* bugfix related to incorrect null verbosity (-v -1)


v1.02
+ support of platypi interactions

v1.01
+ makes clear that gap jumps are activated by default when gap ratio >=30%
* rewrote the command help (-h) to make it more clear

v1.00
+ Initial public release