remove example lateral-transfer-by-replacement

examples/lateral-transfer-by-replacement/README

-In this example, when an individual reproduces, there is a 10% probability
-that a lateral transfer is attempted. If yes, a donor individual is randomly chosen
-in the population. A segment of its chromosome is copied and transferred in the
-recipient individual (the one which was reproducing). This foreign DNA then replaces
-the homologous segment in the recipient chromosome. This is a way to perform allelic 
-recombination.
-
-To run this example for 200 generations, type the following commands:
-aevol_create
-aevol_run -n 200
-
-Then you can look at all the transfer events that took place by typing:
-more log_transfer.out
-
-You can also reconstruct the ancestral lineage of the final best individual and the
-mutations that occurred on this lineage, to see whether some transfer events were 
-selected:
-aevol_misc_lineage -b 0 -e 200
-aevol_misc_fixed_mutations -f lineage-b000000-e000200-i...-r...ae 
-more stats/fixedmut-b000000-e000200-i...-r...out
- 
-
-
-Details:
-
-A transfer attempt starts by searching for a short region of strong sequence similarity
-between the recipient chromosome and the donor chromosome. If none is found, there
-will be no transfer. If on the contrary an alignment is found with a sufficient 
-score, this initial alignment is extended until there is no sequence similarity 
-anymore or until a random event stops the extension -- at each extension step, there 
-is a probability called REPL_TRANSFER_DETACH_RATE to stop the extension even if there 
-is some sequence similarity. 

examples/lateral-transfer-by-replacement/param.in

-###################################
-#         AEVOL PARAMATERS        #
-###################################
-
-##### 1. Initial setup ############
-SEED                    7250909
-WORLD_SIZE              25 20
-INIT_POP_SIZE           500
-INIT_METHOD             ONE_GOOD_GENE CLONE
-CHROMOSOME_INITIAL_LENGTH  5000
-
-##### 2. Selection ################
-SELECTION_SCHEME        fitness   750
-
-##### 3. Mutation rates ###########
-POINT_MUTATION_RATE     5e-6
-SMALL_INSERTION_RATE    5e-6
-SMALL_DELETION_RATE     1e-5
-MAX_INDEL_SIZE          6
-
-##### 4. Rearrangement rates (w/o alignements)
-DUPLICATION_RATE        5e-5
-DELETION_RATE           5e-5
-TRANSLOCATION_RATE      5e-5
-INVERSION_RATE          5e-5
-
-##### 5. Population Structure #####
-
-##### 6. Target function ##########
-ENV_SAMPLING      300
-ENV_ADD_GAUSSIAN  0.5   0.2   0.05
-ENV_ADD_GAUSSIAN  0.5   0.6   0.05
-ENV_ADD_GAUSSIAN  0.5   0.8   0.05
-
-MAX_TRIANGLE_WIDTH  0.005
-
-##### 7. Recording ################
-RECORD_TREE             true
-TREE_STEP               50
-MORE_STATS              false
-DUMP_STEP               0
-BACKUP_STEP             100
-LOG                     BARRIER TRANSFER
-
-##### 8. Environment variation ####
-ENV_VARIATION           autoregressive_height_variation 0.05 5000 123840
-
-##### 9. Phenotypic axis ##########
-ENV_AXIS_FEATURES METABOLISM
-
-##### 10. Secretion ###############
-
-##### 11. Plasmids ################
-ALLOW_PLASMIDS                  false
-WITH_TRANSFER                   true
-TRANSFER_REPL_RATE              0.1
-REPL_TRANSFER_WITH_CLOSE_POINTS true
-REPL_TRANSFER_DETACH_RATE       0.3
-
-##### 12. Alignment ###############
-ALIGN_FUNCTION          SIGMOID 0 40 
-ALIGN_W_ZONE_H_LEN      50
-ALIGN_MAX_SHIFT         20
-ALIGN_MATCH_BONUS       1
-ALIGN_MISMATCH_COST     2
-
-WITH_ALIGNMENTS         false
-# MIN_ALIGN_SCORE         40  
-# MAX_ALIGN_SCORE         100 
-# MAX_SHIFT               20  
-# W_ZONE_H_LEN            50
-
-##### 13. Rearrangement rates (w/ alignements)
-NEIGHBOURHOOD_RATE       1e-1
-DUPLICATION_PROPORTION   5e-5
-DELETION_PROPORTION      5e-5
-TRANSLOCATION_PROPORTION 5e-5
-INVERSION_PROPORTION     5e-5
-
-##### 14. Regulation ##############
-# HILL_SHAPE_N                   4 
-# HILL_SHAPE_THETA               0.5
-# DEGRADATION_RATE               1 
-# DEGRADATION_STEP               0.1
-# INDIVIDUAL_EVALUATION_DATES    NULL
-# INDIVIDUAL_LIFE_TIME           0
-# BINDING_ZEROS_PERCENTAGE       0.75
-# WITH_HEREDITY                  false
-# PROTEIN_PRESENCE_LIMIT         1e-5
-
-##### 15. Random, to be (fully) implemented
-TRANSLATION_COST                0
-