CMakeLists.txt

@@ -23,7 +23,7 @@ IF(NOT NO_DEP_CHECK)
 ENDIF(NOT NO_DEP_CHECK)
 
 IF(NO_DEP_CHECK)
-  MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+  MESSAGE(STATUS "Dependencies checking disabled. Only distribution can be built.")
 ELSE(NO_DEP_CHECK)
 
 
@@ -34,7 +34,7 @@ IF(NOT BUILD_STATIC)
       FORCE)
 ENDIF()
 IF(BUILD_STATIC)
-  MESSAGE("-- Static linkage requested.")
+  MESSAGE(STATUS "Static linkage requested.")
   SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
 ENDIF()
 
@@ -88,10 +88,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "bppsuite")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
 SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 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")

README.md

@@ -78,5 +78,8 @@ Many examples are available in the subdirectory of <tt>Examples</tt>.
 
 ### Documentation 
 
-Documentation can be found at https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
+
+Documentation can be found in one page at: http://bioweb.me/bppsuite-doc
+
+Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
  
\ No newline at end of file

bppsuite.spec

@@ -3,7 +3,7 @@
 URL: https://github.com/BioPP
 
 Name: bppsuite
-Version: 2.4.0
+Version: 2.4.1
 Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
@@ -88,6 +88,7 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/share/man/man1/*.1*
 
 %changelog
+* Wed Aug 15 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1
 * Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

debian/changelog

+bppsuite (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 22 Aug 2018 09:18:13 +0200
+
 bppsuite (2.4.0-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

doc/bppsuite.texi

@@ -1667,8 +1667,34 @@ Concerning the optimization procedure, this choice may entail the non-
 identifiability of several parameters (here the probabilities in model
 3), so the user should be careful about this. 
 
+
+When the submodel is aliased behind a model name, the paths should be
+defined as combinations of the model that is mixed. For example,
+YNGP_M2 is made of 3 YN98 models, depending of three @var{omega}
+values: <1, =1, >1. If we want a site to switch between <1 and >1
+omega values between two sets of branches:
+
+@cartouche
+@example
+nonhomogeneous = general
+nonhomogeneous.number_of_models = 2
+
+model1=YNGP_M2(frequencies=F1X4)
+model2=YNGP_M2(frequencies=F1X4)
+
+model1.nodes_id=0:1
+model2.nodes_id=2:3
+
+site.number_of_paths=3
+site.path1=model1[YN98.omega_1] & model2[YN98.omega_3]
+site.path2=model1[YN98.omega_2] & model2[YN98.omega_2]
+site.path3=model1[YN98.omega_3] & model2[YN98.omega_1]
+
+@end example
+@end cartouche
+
 Another example in the case of mixtures of mixed models, where the
-submodels are defined by their names;
+submodels are defined by their names:
 
 @cartouche
 @example
@@ -1730,6 +1756,17 @@ For nucleotides only, set the G content equal to the C content.
 Full parametrization. Contains N free parameters, where N is equal to the size of the alphabet - 1. For codon models, N is the size of the alphabet - 1 - the number of stop codons, whose frequencies are set to 0.
 For nucleotide sequences, theta is the GC content, theta1 is the proportion of A over A+T, and theta2 is the proportion of G over G+C.
 
+@item Empirical(file=@{path@} [,col=@{int@}])
+Read frequencies from a file. Each frequencies is set as plain column
+in the file. If several columns are in the file, the number of the
+column can be given with @{col@} argument (default: 1).
+
+@item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"])
+Build a protein substitution model from a file in PAML format, and use
+free equilibrium frequencies. 'name' will be used as a parameter
+namespace, including for frequencies.
+
+
 @item Word(frequency=@{frequency set description@})
 
 or