CHANGELOG

FastCodeML 1.3.0:
- Support for trees with length 0 branches
- Supporting rooted trees by unrooting them first
- Support for terminal branches as foreground
- Supporting multiple foreground branches
- More consistent results with codeml by unifying initial points and distributions
-- Detail
- Better installations guide, standard output and command line options
- Correcting bugs in converting external and internal proportions

FastCodeML 1.2.0:
- (Major) BG/Q compatibility (detail below)
- (Minor) Removal of -np option (now controlled by -nt), cleanup of std::cout in main.
---DETAIL
- BranchSiteModel.cpp
	> l.52 int to unsigned int
	> l379-l386 mFixedBranchLength switch logic (uncommitted change).
- BranchSiteModel.h 
	> Init order changed
- CMakeLists.txt
	> Boost required at 1.55
- CmdLine.cpp + .h
	> Removed OPT_FORCE_SERIAL as command line option (replaced with -nt = 1)
	> Changed init order
- CompilerHints.h 
	> Added #defines for __xlC__
- Forest.cpp + .h 
	> Formatting + cleaning constructor and mAllBranchesFG member.
- Genes.cpp 
	> Formatting output stream.
- WriteResults.cpp
	> Output to cout does not compile on BG/Q - commented out.
- blas.h
	> _BGQ_COMPILER #defines
- fast.cpp
	> Removal of -np option.
- SETPATHS - example explaining how to set envionment variables per machine.

FastCodeML 1.1.0:
- Few corrections to accept pipe character also in sequence names
- New option to fixed branch lengths (-bl)
- New option fo manage easily number of threads (-nt)
- Codeml optimizer is by default (-m 22)
- Show branch lengths in default output
- Show p0/p1/p2a/p2b & w0/kappa in default output
- Display a warning if tree is rooted
- Display FastCodemL version

FastCodeML 1.0.1:
- Added text files for LICENSE etc. Source files remain unchanged.
- Version 1.0.1 contains additional information files, the sources are
  unchanged with respect to 1.0.0.

FastCodeML 1.0.0:
- Initial release