diff --git a/examples/basic_stdlist/param.in b/examples/basic/param.in similarity index 98% rename from examples/basic_stdlist/param.in rename to examples/basic/param.in index 7fc56a1740ef33d331e33fa4cb55c056a319e3f7..8c782b57b2f81ef8edaee954d629000c96e5f3f7 100644 --- a/examples/basic_stdlist/param.in +++ b/examples/basic/param.in @@ -42,7 +42,7 @@ MAX_TRIANGLE_WIDTH 0.033333333 ##### 7. Recording ################ BACKUP_STEP 1000 TREE_STEP 100 -RECORD_TREE true +RECORD_TREE false RECORD_LIGHT_TREE false MORE_STATS false diff --git a/examples/complex_env/param.in b/examples/complex_env/param.in new file mode 100644 index 0000000000000000000000000000000000000000..1bccb73bc334d77d79384148a2052d9f844ce3e4 --- /dev/null +++ b/examples/complex_env/param.in @@ -0,0 +1,168 @@ +################################### +# AEVOL PARAMATERS # +################################### + +##### 1. Initial setup ############ +STRAIN_NAME basic_example +SEED 51456165 +INIT_POP_SIZE 1024 +WORLD_SIZE 32 32 +INIT_METHOD ONE_GOOD_GENE CLONE +CHROMOSOME_INITIAL_LENGTH 5000 +FUZZY_FLAVOR 1 + +##### 2. Selection ################ +SELECTION_SCHEME fitness_proportionate 750 + +##### 3. Mutation rates ########### +POINT_MUTATION_RATE 5e-5 +SMALL_INSERTION_RATE 5e-5 +SMALL_DELETION_RATE 5e-5 +MAX_INDEL_SIZE 6 + +##### 4. Rearrangement rates (w/o alignements) +WITH_ALIGNMENTS false +DUPLICATION_RATE 5e-5 +DELETION_RATE 5e-5 +TRANSLOCATION_RATE 5e-5 +INVERSION_RATE 5e-5 + +##### 7. Recording ################ +BACKUP_STEP 1000 +RECORD_TREE false +MORE_STATS true + +#################################################################################### +# Regulation +#################################################################################### +HILL_SHAPE_N 4 +HILL_SHAPE_THETA 0.5 +DEGRADATION_RATE 1 +NB_DEGRADATION_STEP 10 +INDIVIDUAL_EVALUATION_AGES 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 +#EVAL_STEP 1 Ã trouver +BINDING_ZEROS_PERCENTAGE 0.75 +#permit to choose wheter we want to run the simulation with a random binding matrix or not +RANDOM_BINDING_MATRIX false +WITH_HEREDITY false +PROTEIN_PRESENCE_LIMIT 1e-2 + + + + + + +#################################################################################### +# Environments +#################################################################################### +############ Target function ########## +ENV_SAMPLING 300 +MAX_TRIANGLE_WIDTH 0.033333333 +ENV_VARIATION switch_in_a_list 0.1 + +NB_ENVIRONMENTS 16 +ENV_ADD_GAUSSIAN 1 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 1 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 1 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 1 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 2 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 2 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 2 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 2 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 3 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 3 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 3 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 3 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 4 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 4 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 4 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 4 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 5 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 5 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 5 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 5 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 6 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 6 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 6 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 6 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 7 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 7 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 7 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 7 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 8 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 8 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 8 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 8 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 9 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 9 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 9 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 9 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 10 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 10 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 10 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 10 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 11 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 11 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 11 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 11 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 12 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 12 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 12 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 12 0.5 0.8 0.05 +ENV_ADD_GAUSSIAN 13 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 13 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 13 0.5 0.6 0.05 +ENV_ADD_GAUSSIAN 13 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 14 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 14 0.5 0.4 0.05 +ENV_ADD_GAUSSIAN 14 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 14 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 15 0.5 0.2 0.05 +ENV_ADD_GAUSSIAN 15 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 15 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 15 0.5 0.85 0.05 +ENV_ADD_GAUSSIAN 16 0.5 0.25 0.05 +ENV_ADD_GAUSSIAN 16 0.5 0.45 0.05 +ENV_ADD_GAUSSIAN 16 0.5 0.65 0.05 +ENV_ADD_GAUSSIAN 16 0.5 0.85 0.05 + + +#################################################################################### +# List of signals +#################################################################################### +CREATE_SIGNAL h0 w0 h1 m1 w0 h1 m0 h0 h1 w0 h0 m1 h1 h1 m1 m0 h0 w0 h1 m1 w0 h1 m0 h0 h1 w0 h0 m1 h1 h1 m1 m0 h1 m0 m1 +CREATE_SIGNAL m0 h0 m1 h1 m1 w0 m0 m1 m0 h0 m1 h1 w0 h0 h0 h1 m1 m0 h1 w0 h1 h0 m1 h1 m0 w0 w0 m0 m1 w0 w0 h1 h0 w0 h1 h0 h0 m0 h0 w0 h0 m1 m0 w0 h1 w0 w0 h1 m0 +CREATE_SIGNAL h0 h0 h0 w0 m0 m1 m0 h1 h0 m0 h0 m1 h1 w0 h1 h0 m1 h1 m0 w0 w0 m0 w0 h0 h1 m1 w0 m0 m1 m0 w0 h1 h0 m0 h0 m1 h1 w0 h0 w0 m0 m1 m0 w0 h1 h0 w0 w0 h1 +CREATE_SIGNAL h1 h1 m0 w0 w0 h1 m1 h1 h1 m1 m0 w0 m1 m0 m0 w0 m0 h0 m0 h0 w0 h0 m0 h0 h1 m1 h0 h1 w0 h0 h1 m1 h1 m1 m0 +ENV_ADD_SIGNAL 2 1 +ENV_ADD_SIGNAL 3 2 +ENV_ADD_SIGNAL 4 3 +ENV_ADD_SIGNAL 5 4 +ENV_ADD_SIGNAL 6 1 +ENV_ADD_SIGNAL 6 2 +ENV_ADD_SIGNAL 7 1 +ENV_ADD_SIGNAL 7 3 +ENV_ADD_SIGNAL 8 1 +ENV_ADD_SIGNAL 8 4 +ENV_ADD_SIGNAL 9 2 +ENV_ADD_SIGNAL 9 3 +ENV_ADD_SIGNAL 10 2 +ENV_ADD_SIGNAL 10 4 +ENV_ADD_SIGNAL 11 3 +ENV_ADD_SIGNAL 11 4 +ENV_ADD_SIGNAL 12 1 +ENV_ADD_SIGNAL 12 2 +ENV_ADD_SIGNAL 12 3 +ENV_ADD_SIGNAL 13 1 +ENV_ADD_SIGNAL 13 2 +ENV_ADD_SIGNAL 13 4 +ENV_ADD_SIGNAL 14 1 +ENV_ADD_SIGNAL 14 3 +ENV_ADD_SIGNAL 14 4 +ENV_ADD_SIGNAL 15 2 +ENV_ADD_SIGNAL 15 3 +ENV_ADD_SIGNAL 15 4 +ENV_ADD_SIGNAL 16 1 +ENV_ADD_SIGNAL 16 2 +ENV_ADD_SIGNAL 16 3 +ENV_ADD_SIGNAL 16 4