New upstream version 2.4.1

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)

      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()

# 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")

### 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

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

%{_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

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

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