AEVOL(1)

NAME
aevol - an in silico experimental evolution platform

SYNOPSIS
aevol_misc_mutagenesis -h | --help
aevol_misc_mutagenesis -V | --version
aevol_misc_mutagenesis -g GENER [-i INDEX | -r RANK] [-m MUTATIONTYPE] [-n NBMUTANTS]

DESCRIPTION
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.

aevol_misc_mutagenesis
    creates and evaluates single mutants of an individual saved in a backup, by default the best of its generation. Use option -g to specify the generation number contanining the individual of interest. There must have been a backup of the population at this generation. For example, if the program is called with the option -g 4000, there must be a file called pop_004000.ae in the populations directory. Use either the -r or the -i option to select another individual than the best one: with -i, you have to provide the ID of the individual, and with -r the rank (1 for the individual with the lowest fitness, N for the fittest one). The type of mutations to perform must be specified with the -m option. Choose 0 to create mutants with a point mutation, 1 for a small insertion, 2 for a small deletion, 3 for a duplication, 4 for a large deletion, 5 for a translocation or 6 for an inversion. For the point mutations, all single mutants will be created and evaluated. For the other mutation types, an exhaustive mutagenesis would take too much time, hence only a sample of mutants (1000 by default) will be generated. Use option -n to specify another sample size. The output file will be placed in a subdirectory called analysis-generationNUMGENER.

OPTIONS

-h, --help
    print help, then exit

-V, --version
    print version number, then exit

-g, --gener NUMGENER
generation of the backup containing the individual of interest

-i, --index INDEX
index of individual of interest

-r, --rank RANK
rank of individual of interest. Default = size of the population (fittest individual)

-m, --mutation-type MUTATIONTYPE
integer type of the mutation carried by each mutant: 0 for a point mutation, 1 for a small insertion, 2 for small deletions, 3 for a duplication, 4 for a large deletion, 5 for a translocation or 6 for an inversion

-n, --nb-mutants NBMUTANTS
number of single mutants to create and evaluate. Default = 1000. Note that this option is ignored in the case of point mutations, where all single mutants are created (exhaustive mutagenesis)

SEE ALSO
aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps, aevol_misc_robustness