Commit 27c31817 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.0

parent f51eb03e

CMakeLists.txt

+7 −6
Original line number Diff line number Diff line
@@ -61,7 +61,8 @@ else () 
  # Generate command line args (always add -c to output compressed file to stdout)

  if (${COMPRESS_PROGRAM} STREQUAL "gzip")

    # -n for no timestamp in files (reproducible builds)

    set (COMPRESS_ARGS -c -n)

    # -9 for maximum compression (lintian error)

    set (COMPRESS_ARGS -c -n -9)

  else ()

    set (COMPRESS_ARGS -c)

  endif ()
@@ -74,8 +75,8 @@ if (CMAKE_INSTALL_PREFIX) 
endif (CMAKE_INSTALL_PREFIX)



include (GNUInstallDirs)

find_package (bpp-phyl 11.0.0 REQUIRED)

find_package (bpp-popgen 7.0.0 REQUIRED)

find_package (bpp-phyl 12.0.0 REQUIRED)

find_package (bpp-popgen 8.0.0 REQUIRED)



# Subdirectories

add_subdirectory (bppSuite)
@@ -87,10 +88,10 @@ ENDIF(NO_DEP_CHECK) 
# Packager

SET(CPACK_PACKAGE_NAME "bppsuite")

SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")

SET(CPACK_PACKAGE_VERSION "2.3.1")

SET(CPACK_PACKAGE_VERSION "2.4.0")

SET(CPACK_PACKAGE_VERSION_MAJOR "2")

SET(CPACK_PACKAGE_VERSION_MINOR "3")

SET(CPACK_PACKAGE_VERSION_PATCH "1")

SET(CPACK_PACKAGE_VERSION_MINOR "4")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite")

SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")

SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

ChangeLog

+7 −0
Original line number Diff line number Diff line 
19/03/18 -*- Version 2.4.0 -*-



19/02/18 Julien Dutheil

* Bug fixed in bppPopStats: dN and dS were inverted!



10/12/17 -*- Version 2.3.2 -*-



06/11/17 Julien Dutheil

* Added estimation of kappa to bppPopStats + bugs fixed

Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp

+1 −1
Original line number Diff line number Diff line
@@ -95,7 +95,7 @@ optimization.final = none 
optimization.verbose = 3



# Parameters to ignore (for instance equilibrium frequencies)

optimization.ignore_parameter = 

optimization.ignore_parameters = 



# Maximum number of likelihood evaluations:

optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/CladeModel/ML.bpp

+1 −1
Original line number Diff line number Diff line
@@ -102,7 +102,7 @@ optimization.final = none 
optimization.verbose = 3



# Parameters to ignore (for instance equilibrium frequencies)

optimization.ignore_parameter = 

optimization.ignore_parameters = 



# Maximum number of likelihood evaluations:

optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/M0/ML.bpp

+1 −1
Original line number Diff line number Diff line
@@ -87,7 +87,7 @@ optimization.final = none 
optimization.verbose = 3



# Parameters to ignore (for instance equilibrium frequencies)

optimization.ignore_parameter = 

optimization.ignore_parameters = 



# Maximum number of likelihood evaluations:

optimization.max_number_f_eval = 10000