.gitignore

@@ -17,19 +17,23 @@ src/aevol_propagate
 src/aevol_run
 src/libaevol/SFMT-src-1.4/jump/.dirstamp
 *.a
-src/post_treatments/aevol_misc_ancstats
-src/post_treatments/aevol_misc_compute_pop_stats
+src/post_treatments/aevol_misc_ancestor_robustness
+src/post_treatments/aevol_misc_ancestor_stats
 src/post_treatments/aevol_misc_create_eps
 src/post_treatments/aevol_misc_extract
-src/post_treatments/aevol_misc_fixed_mutations
-src/post_treatments/aevol_misc_gene_families
 src/post_treatments/aevol_misc_lineage
 src/post_treatments/aevol_misc_robustness
 src/post_treatments/aevol_misc_mutagenesis
+src/post_treatments/aevol_misc_view
 src/post_treatments/aevol_misc_template
 src/post_treatments/aevol_misc_view_generation
 *.o
 
+# ignore build dir
+build/**
+
+# ignore .idea dir (clion config)
+.idea/**
 
 # ignore the files that are generated from the user guide source
 doc/user_guide/user_manual.aux
@@ -41,11 +45,12 @@ doc/user_guide/user_manual.toc
 # ignore performance records
 perf.data*
 
-
-
 # ignore example generated files
 # i.e. ignore everything under examples directory
 examples/*/**
 # but consider param.in files
 !examples/**/param.in
 !examples/**/README
+
+#ignore the tmp dir
+tmp/**

CMakeLists.txt

-cmake_minimum_required(VERSION 3.2)
-project(aevol_regul)
+# ============================================================================
+# Require minimal version of cmake
+# ============================================================================
+cmake_minimum_required(VERSION 3.0.2)
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 
-set(SOURCE_FILES main.cpp)
-add_executable(aevol_regul ${SOURCE_FILES} src/libaevol/HabitatFactory.cpp src/libaevol/HabitatFactory.h)
+# ============================================================================
+# Set project name and languages
+# ============================================================================
+project(aevol VERSION 5.0 LANGUAGES C CXX)
+add_definitions(-DVERSION="${PROJECT_VERSION}")
+
+# Temporary stuff to be fully integrated into CMake
+add_definitions(-DSFMT_MEXP=607)
+add_definitions(-D__X11)
+add_definitions(-DDEBUG)
+
+FIND_PACKAGE ( X11 REQUIRED )
+IF ( X11_FOUND )
+      INCLUDE_DIRECTORIES ( ${X11_INCLUDE_DIR} )
+      LINK_LIBRARIES ( ${X11_LIBRARIES} )
+ENDIF ( X11_FOUND )
+
+
+# ============================================================================
+# Get GNU standard installation directories (GNUInstallDirs module)
+# ============================================================================
+include(GNUInstallDirs)
+
+
+# ============================================================================
+# Tell CMake where to look for custom modules
+# ============================================================================
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
+
+# ============================================================================
+# Tell cmake where to put binary files.
+# By GNU standards "executable programs that users can run" should go in
+# bindir a.k.a ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}
+# and "executable programs to be run by other programs rather than by users"
+# in libexecdir a.k.a ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBEXECDIR}
+# ============================================================================
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
+
+
+# ============================================================================
+# Set build type specific compilation flags
+# ============================================================================
+set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -g")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
+
+
+# ============================================================================
+# Tell cmake about subdirectories to look into
+# ============================================================================
+add_subdirectory(src)
+
+
+# ============================================================================
+# Adds the 'dist' target (that will use CPack)
+# ============================================================================
+#add_custom_target(dist COMMAND ${CMAKE_BUILD_TOOL} package_source)
+
+
+# ============================================================================
+# Add the 'uninstall' target (uses a custom script)
+# ============================================================================
+configure_file(
+    "${PROJECT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
+    "${CMAKE_BINARY_DIR}/cmake_uninstall.cmake"
+    IMMEDIATE @ONLY)
+
+add_custom_target(uninstall
+    COMMAND ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/cmake_uninstall.cmake)

configure.ac

@@ -22,9 +22,6 @@ AC_CONFIG_MACRO_DIR([m4])
 # We want to use automake
 AM_INIT_AUTOMAKE
 
-# Define C++ compilator
-AC_PROG_CXX([gcc,icc])
-
 # Detect C++11 or C++14
 AX_CXX_COMPILE_STDCXX_14([noext],[optional])
 AX_CXX_COMPILE_STDCXX_11([noext])
@@ -48,6 +45,11 @@ AM_PROG_CC_C_O
 # Print warning if openmp not found
 AC_CHECK_HEADER([omp.h], , [AC_MSG_WARN([openmp not found - continuing without openmp support])])
 
+# Check for boost
+AX_BOOST_BASE([1.55],, [AC_MSG_ERROR([boost not found, please check that you have boost installed on your system and retry])])
+AX_BOOST_SYSTEM
+AX_BOOST_FILESYSTEM
+
 # Initialize configure-time defined flags
 AC_SUBST(AEVOLCPPFLAGS, "") # C PreProcessor flags
 AC_SUBST(AEVOLCXXFLAGS, "$OPENMP_CXXFLAGS") # C++ Compile flags
@@ -97,12 +99,10 @@ AC_SUBST(PTHREAD_LIBS)
 
 #   ************************ --without-x option *********************
 #
-#   When this option is set, typing make will produce aevol and
-#   most post-treatment programs, but not aevol_X11.
+#   When this option is set, running make will produce aevol and
+#   most post-treatment programs without visualization capabilities
 #   This is useful if we want to run computations on a cluster where the
-#   X libraries are not present. If, on the contrary, we type ./configure
-#   without this option, then typing make will produce aevol_X11 and
-#   view_generation_X11 (and the other post-treatment programs).
+#   X libraries are not present.
 
 AC_MSG_CHECKING([whether to enable graphical outputs])
 AC_ARG_WITH(x, [  --without-x to disable graphical output], , with_x=yes)

dev-doc/RELEASE_HowTo

@@ -5,10 +5,14 @@ RELEASE HowTo
   -> in all the manpages (update date too)
   -> in the user guide (if needed)
 
-2) Write an entry in the NEWS file
+2) Write an entry in the NEWS file for users
+   and in ChangeLog for developers.
 
-3) [TEMPORAIRE tant que les tests sont quasi inexistants]
-  -> Virer les tests
+3) [TEMPRORARY as long as tests are scarce]
+  -> Remove tests directories
+  -> Remove references to tests in configure.ac, src/Makefile.am
+
+3') Clean up examples: remove all computed data files
 
 4) Run the following commands (from aevol root dir)
   -> autoreconf
@@ -17,7 +21,6 @@ RELEASE HowTo
 
   This will generate a file called aevol-X.Y.tar.gz in aevol root dir
 
-
 5) Add a version in the "files" section of the forge
   -> In the "files" section click on the link to "create a new version"
   -> Fill in the form with

doc/Makefile.am

@@ -9,10 +9,10 @@ endif
 
 # Man pages
 dist_man1_MANS = aevol_create.1 aevol_run.1 aevol_modify.1 aevol_propagate.1
-dist_man1_MANS += aevol_misc_lineage.1 aevol_misc_ancstats.1
+dist_man1_MANS += aevol_misc_lineage.1 aevol_misc_ancestor_stats.1
 dist_man1_MANS += aevol_misc_robustness.1 aevol_misc_compute_pop_stats.1
-dist_man1_MANS += aevol_misc_view_generation.1 aevol_misc_create_eps.1
-dist_man1_MANS += aevol_misc_extract.1 aevol_misc_fixed_mutations.1
+dist_man1_MANS += aevol_misc_view.1 aevol_misc_create_eps.1
+dist_man1_MANS += aevol_misc_extract.1
 dist_man1_MANS += aevol_misc_gene_families.1
 
 

doc/aevol_create.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_create \-h
 or
@@ -11,14 +11,14 @@ or
 or
 .B \-\-version
 .br
-.B aevol_create \fR[\fB\-v\fR] \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-c\fI CFILE\fR] \fR[\fB\-p\fI PFILE\fR]
+.B aevol_create \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-C\fI CHROM_FILE\fR] \fR[\fB\-p\fI PLASMID_FILE\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
 .B aevol_create
 create an experiment with setup as specified in
-.I param_file
+.I PARAM_FILE
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -32,19 +32,15 @@ print version number, then exit
 .br
 specify parameter file (default: param.in)
 .HP
-.B \-o, \-\-out
-.I OUTDIR
-.br
-specify output directory (default "./")
 .HP
-.B \-c, \-\-chromosome
-.I CFILE
+.B \-C, \-\-chromosome
+.I CHROM_FILE
 .br
 load chromosome from given text file instead of generating it
 .HP
-.B \-p, \-\-plasmid
-.I PFILE
+.B \-P, \-\-plasmid
+.I PLASMID_FILE
 .br
-load plasmid from given text file instead of generating it (params must allow plasmids)
+load plasmid from given text file instead of generating it
 .SH "SEE ALSO"
 .B aevol_run, aevol_modify, aevol_propagate

doc/aevol_misc_ancstats.1 → doc/aevol_misc_ancestor_stats.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
-.B aevol_misc_ancstats \-h
+.B aevol_misc_ancestor_stats \-h
 |
 .B \-\-help
 .br
-.B aevol_misc_ancstats \-V
+.B aevol_misc_ancestor_stats \-V
 |
 .B \-\-version
 .br
-.B aevol_misc_ancstats \fB\-f\fI LINEAGE_FILE
+.B aevol_misc_ancestor_stats \fILINEAGE_FILE \fR[\fB\-FMv\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
-.B aevol_misc_ancstats
-issues statistics for the line of descent of a given individual.
+.B aevol_misc_ancestor_stats
+issues statistics for the line of descent described in LINEAGE_FILE.
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -25,10 +25,14 @@ print help, then exit
 .TP
 .B \-V, \-\-version
 print version number, then exit
-.HP
-.B \-f, \-\-file
-.I  LINEAGE_FILE
-.br
-specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
+.TP
+.B \-F, \-\-full-check
+perform genome checks whenever possible
+.TP
+.B \-M, \-\-trace-mutations
+outputs the fixed mutations (in a separate file)
+.TP
+.B \-v, \-\-verbose
+be verbose
 .SH "SEE ALSO"
 .B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_misc_create_eps.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_misc_create_eps \-h
 |
@@ -11,13 +11,13 @@ aevol \- an in silico experimental evolution platform
 |
 .B \-\-version
 .br
-.B aevol_misc_create_eps \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fB\-g\fI GENER
+.B aevol_misc_create_eps \fR[\fB\-t\fI TIMESTEP\fR] \fR[\fB\-I\fI INDEX\fR | \fB\-R\fI RANK\fR] \fR[\fB\-v\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
 .B aevol_misc_create_eps
-produces several eps files describing an individual of this population
+creates EPS files with the triangles, the positive and negative	profiles, the phenotype, the CDS and the mRNAs of the individual of interest.
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -26,19 +26,23 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-i, \-\-index
+.B \-t, \-\-timestep
+.I TIMESTEP
+.br
+specify timestep of the individual of interest
+.br
+default: that contained in file last_gener.txt, if any
+.HP
+.B \-I, \-\-index
 .I  INDEX
 .br
-specify the index (ID in current generation) of the individual
+specify the index of the individual of interest
 .HP
-.B \-r, \-\-rank
+.B \-R, \-\-rank
 .I  RANK
 .br
-specify the rank of the individual
-.HP
-.B \-g, \-\-gener
-.I  GENER
+specify the rank of the individual of interest
 .br
-specify the generation of the individual
+default: best individual
 .SH "SEE ALSO"
 .B aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_misc_extract.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_misc_extract \-h
 |
@@ -11,7 +11,7 @@ aevol \- an in silico experimental evolution platform
 |
 .B \-\-version
 .br
-.B aevol_misc_extract \fR[\fB\-r\fI GENER\fR | \fB\-p\fI POP_FILE\fR] \fR[\fB\-t\fI PHEN_FILE\fR] \fR[\fB\-s\fI SEQ_FILE\fR] \fR[\fB\-g\fI NUM_GU\fR] \fR[\fB\-b\fR]
+.B aevol_misc_extract \fR[\fB\-t\fI TIMESTEP\fR] \fR[\fB\-S\fI SEQ_FILE\fR] \fR[\fB\-T\fI TRIANGLE_FILE\fR] \fR[\fB\-U\fI NUM_GU\fR] \fR[\fB\-a\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
@@ -26,33 +26,32 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-r
-.I  GENER
+.B \-t
+.I TIMESTEP
 .br
-read generation GENER from a full aevol backup
+specify timestep of the individual(s) of interest
 .HP
-.B \-p
-.I  POP_FILE
+.B \-S
+.I  SEQ_FILE
 .br
-read the population saved in population file POP_FILE
+extract sequences into file SEQ_FILE
 .HP
-.B \-t
-.I  PHEN_FILE
+.B \-T
+.I  TRIANGLE_FILE
 .br
-extract and save some infos about the phenotypes of the individuals to file PHEN_FILE
+extract phenotypic data into file TRIANGLE_FILE
 .HP
-.B \-s
-.I  SEQ_FILE
+.B \-U
+.I  NUM_GU
 .br
-extract and save the sequences of the individuals to file SEQ_FILE
-.HP
-.B \-g
-.I  num_gu
+only treat genetic unit #NUM_GU
 .br
-only treat this genetic unit (by default: treat all genetic units)
+default: treat all genetic units
 .HP
-.B \-b
+.B \-a
+.br
+treat all the individuals
 .br
-only treat the best individual
+default: treat only the best
 .SH "SEE ALSO"
 .B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_misc_fixed_mutations.1

-./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_fixed_mutations \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_fixed_mutations \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_fixed_mutations \fB\-f\fI LINEAGE_FILE
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_fixed_mutations
-issues the detailed list of mutations that occurred in the lineage of a given individual
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-f, \-\-file
-.I  LINEAGE_FILE
-.br
-specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_misc_lineage.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_misc_lineage \-h
 |
@@ -11,13 +11,13 @@ aevol \- an in silico experimental evolution platform
 |
 .B \-\-version
 .br
-.B aevol_misc_lineage \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
+.B aevol_misc_lineage \fR[\fB\-b\fI TIMESTEP\fR] \fR[\fB\-e\fI TIMESTEP\fR] \fR[\fB\-I\fI INDEX\fR | \fB\-R\fI RANK\fR] \fR[\fB\-F\fR] \fR[\fB\-v\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
 .B aevol_misc_lineage
-allows for the reconstruction of the lineage of a given individual. Requires the tree to have been recorded during evolution.
+reconstruct the lineage of a given individual from the tree files
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -26,24 +26,33 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-i, \-\-index
+.B \-b, \-\-begin
+.I  TIMESTEP
+.br
+specify time t0 up to which to reconstruct the lineage
+.HP
+.B \-e, \-\-end
+.I  TIMESTEP
+.br
+specify time t_end of the indiv whose lineage is to be reconstructed
+.HP
+.B \-I, \-\-index
 .I  INDEX
 .br
-specify the index (ID in current generation) of the individual whose lineage is to be reconstructed
+specify the index of the indiv whose lineage is to be reconstructed
 .HP
-.B \-r, \-\-rank
+.B \-R, \-\-rank
 .I  RANK
 .br
-specify the rank of the individual whose lineage is to be reconstructed
+specify the rank of the indiv whose lineage is to be reconstructed
+default: best individual
 .HP
-.B \-b, \-\-begin
-.I  GENER
+.B \-F, \-\-full-check
 .br
-specify the generation up to which the lineage is to be reconstructed
+perform genome checks whenever possible
 .HP
-.B \-e, \-\-end
-.I  GENER
+.B \-v, \-\-verbose
 .br
-specify the generation of the individual whose lineage is to be reconstructed
+be verbose
 .SH "SEE ALSO"
 .B aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_misc_mutagenesis.1

@@ -69,4 +69,4 @@ number of single mutants to create and evaluate. Default = 1000. Note that this
 
 
 .SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps, aevol_misc_robustness
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view, aevol_misc_create_eps, aevol_misc_robustness

doc/aevol_misc_robustness.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
-.B aevol_misc_robustness \-h
-|
-.B \-\-help
+.B aevol_misc_robustness \-h \fR|\fB \-\-help
 .br
-.B aevol_misc_robustness \-V
-|
-.B \-\-version
+.B aevol_misc_robustness \-V \fR|\fB \-\-version
 .br
-.B aevol_misc_robustness \fR\fB\-g\fI GENER\fR [\fB\-n\fI NBCHILDREN] \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR]
+.B aevol_misc_robustness \fR[\fB\-t\fI TIMESTEP\fR] \fR[\fB\-I\fI INDEX\fR | \fB\-R\fI RANK\fR] [\fB\-n\fI NB_MUTANTS]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
@@ -27,25 +23,26 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-g, \-\-gener
-.I  GENER
+.B \-t, \-\-timestep
+.I  TIMESTEP
 .br
-specify the generation number for which the robustness statistics are desired
+specify timestep of the individual of interest
 .HP
-.B \-n, \-\-nb\-children
-.I  NBCHILDREN
-.br
-specify the number of reproductions to simulate for each individual
-.HP
-.B \-i, \-\-index
+.B \-I, \-\-index
 .I  INDEX
 .br
-specify the index (ID in current generation) of the individual for whom detailed reproduction statistics are desired
+specify the index of the individual of interest
 .HP
-.B \-r, \-\-rank
+.B \-R, \-\-rank
 .I  RANK
 .br
-specify the rank of the individual for whom detailed reproduction statistics are desired
+specify the rank of the individual of interest
+default: best individual
+.HP
+.B \-n, \-\-nb\-mutants
+.I  NB_MUTANTS
+.br
+specify the number of mutants to be generated
 
 .SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps
+.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_ancestor_robustness

doc/aevol_misc_view_generation.1 → doc/aevol_misc_view.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
-.B aevol_misc_view_generation \-h
+.B aevol_misc_view \-h
 |
 .B \-\-help
 .br
-.B aevol_misc_view_generation \-V
+.B aevol_misc_view \-V
 |
 .B \-\-version
 .br
-.B aevol_misc_view_generation \fB\-g\fI GENER
+.B aevol_misc_view \fB\-t\fI TIMESTEP
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
-.B aevol_misc_view_generation
-allows one to visualize a generation using the exact same graphical outputs used in aevol_run.
+.B aevol_misc_view
+view the simulation at the provided timestep
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -26,9 +26,11 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-g, \-\-gener
-.I  GENER
+.B \-t, \-\-timestep
+.I TIMESTEP
 .br
-specify generation to visualize (default 0)
+specify timestep to display
+.br
+default: that contained in file last_gener.txt, if any
 .SH "SEE ALSO"
 .B aevol_create, aevol_modify, aevol_propagate, aevol_run

doc/aevol_modify.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_modify \-h
 or
@@ -11,14 +11,14 @@ or
 or
 .B \-\-version
 .br
-.B aevol_modify \-g\fI GENER \fR[\fB\-f\fI param_file\fR]
+.B aevol_modify \fR[\fB\-T\fI TIMESTEP\fR] \fR[\fB\-F\fI PARAM_FILE\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
 .B aevol_modify
 modify an experiment as specified in
-.I param_file
+.I PARAM_FILE
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -27,13 +27,13 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-g, \-\-gener
-.I GENER
+.B \-t, \-\-timestep
+.I TIMESTEP
 .br
-specify generation number
+specify timestep
 .HP
 .B \-f, \-\-file
-.I param_file
+.I PARAM_FILE
 .br
 specify parameter file (default: param.in)
 .SH "SEE ALSO"

doc/aevol_propagate.1

-\"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+./"test with man -l <file>
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_propagate \-h
 or
@@ -11,15 +11,13 @@ or
 or
 .B \-\-version
 .br
-.B aevol_propagate \fR[\fB\-v\fR]  \fR[\fB\-g\fI GENER\fR]  \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-S\fI GENERALSEED\fR]
-.br
-.B aevol_propagate \fR[\fB\-v\fR]  \fR[\fB\-g\fI GENER\fR]  \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-s\fI SELSEED\fR]   \fR[\fB\-m\fI MUTSEED\fR]   \fR[\fB\-t\fI STOCHSEED\fR]   \fR[\fB\-e\fI ENVVARSEED\fR]   \fR[\fB\-n\fI ENVNOISESEED\fR]
+.B aevol_propagate \fR[\fB\-t\fI TIMESTEP\fR] \fR[\fB\-K\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-v\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
 .TP
 .B aevol_propagate
-creates a fresh copy of the experiment as it was at the given generation. The generation number of the copy will be reset to 0. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. You can use the option -S to do so. In this case, the random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). Alternatively, to change the random drawings for specific random processes only, do not use -S but the options -m, -s, -t, -e, -n (see below).
+creates a fresh copy of the experiment as it was at the given timestep. The timestep of the copy will be reset to 0.
 .SH OPTIONS
 .TP
 .B \-h, \-\-help
@@ -27,54 +25,26 @@ print help, then exit
 .TP
 .B \-V, \-\-version
 print version number, then exit
-.TP
-.B \-v, \-\-verbose
-be verbose
 .HP
-.B \-g, \-\-gener
-.I GENER
+.B \-t, \-\-timestep
+.I TIMESTEP
 .br
-specify generation number
-(default: that contained in file last_gener.txt, if any)
-.HP
-.B \-i, \-\-in
-.I INDIR
+specify timestep to propagate
 .br
-specify input directory (default ".")
+default: that contained in file last_gener.txt, if any
+.TP
+.B \-K, \-\-keep-prng-st
+.br
+do not alter prng states
 .HP
 .B \-o, \-\-out
 .I OUTDIR
 .br
-specify output directory (default "./output")
-.HP
-.B \-S, \-\-general\-seed
-.I GENERALSEED
+specify output directory
 .br
-specify an integer to be used as a seed for random numbers. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different	seed for each simulation, otherwise all simulations will yield exactly the same results. If you specify this general seed, random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). To change the random drawings for a specific random process only, do not use -S but the options below.
-.HP
-.B \-s, \-\-sel\-seed
-.I SELSEED
-.br
-specify an integer as a seed for random numbers needed for selection and migration (if spatial structure is enabled).
-.HP
-.B \-m, \-\-mut\-seed
-.I MUTSEED
-.br
-specify an integer as a seed for random numbers needed for mutations.
-.HP
-.B \-t, \-\-stoch\-seed
-.I STOCHSEED
-.br
-specify an integer as a seed for random numbers needed for stochastic gene expression.
-.HP
-.B \-e, \-\-env\-var\-seed
-.I ENVVARSEED
-.br
-specify an integer as a seed for random numbers needed for environmental variation.
-.HP
-.B \-n, \-\-env\-noise\-seed
-.I ENVNOISESEED
-.br
-specify an integer as a seed for random numbers needed for environmental noise.
+default "./output"
+.TP
+.B \-v, \-\-verbose
+be verbose
 .SH "SEE ALSO"
 .B aevol_create, aevol_run, aevol_modify

doc/aevol_run.1

 ./"test with man -l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
+.TH AEVOL "1" "May 2016" "aevol 5.0" "User Manual"
 .SH NAME
-aevol \- an in silico experimental evolution platform
+Aevol \- an in silico experimental evolution platform
 .SH SYNOPSIS
 .B aevol_run \-h
 |
@@ -11,7 +11,7 @@ aevol \- an in silico experimental evolution platform
 |
 .B \-\-version
 .br
-.B aevol_run \fR[\fB\-r\fI GENER\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
+.B aevol_run \fR[\fB\-b\fI TIMESTEP\fR] \fR[\fB\-e\fI TIMESTEP\fR | \fB\-n\fI NB_TIMESTEP\fR] \fR[\fB\-p\fI NB_THREADS\fR] \fR[\fB\-vwx\fR]
 .SH DESCRIPTION
 .B Aevol
 is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
@@ -26,18 +26,24 @@ print help, then exit
 .B \-V, \-\-version
 print version number, then exit
 .HP
-.B \-r, \-\-resume
-.I  GENER
+.B \-b, \-\-begin
+.I  TIMESTEP
 .br
-specify generation to resume simulation at (default 0)
+specify time t0 to resume simulation at (default read in last_gener.txt)
 .HP
-.B \-n, \-\-nbgener
-.I NB_GENER
+.B \-e, \-\-end
+.I  TIMESTEP
 .br
-specify number of generations to be run (default 1000)
+specify time of the end of the simulation
+.HP
+.B \-n, \-\-nb-timesteps
+.I NB_TIMESTEPS
+.br
+specify number of timesteps to be simulated (default 1000)
 .TP
-.B \-t, \-\-text
-use text files instead of binary files when possible
+.B \-p, \-\-parallel
+.I NB_THREADS
+run on NB_THREADS threads (use -1 for system default)
 .TP
 .B \-v, \-\-verbose
 be verbose

doc/dev/include/styleguide.css

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