Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation use Bio::PopGen::Simulation::GeneticDrift; my $sim = new Bio::PopGen::Simulation::GeneticDrift(-popsize => 40, -alleles => {A => 0.2, B => 0.8}); for(my $i =0 ;$i < 10; $i++ ) { my %f = $sim->next_generation; # get the freqs for each generation } for(my $i =0 ;$i < 10; $i++ ) { # get the allele freqs as part of a Bio::PopGen::Population object my $pop = $sim->next_generation('population'); } A very simple 1 locus multi-allele random drift module, start with an initial set of allele frequency and simulate what happens over time. This isn't really useful for anything in particular yet but will be built upon. See Gillespie JH. (1998) "Population Genetics: a Concise guide." The Johns Hopkins University Press, Baltimore, USA. pp.19-47.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::PopGen::Simulation::GeneticDrift(); Function: Builds a new Bio::PopGen::Simulation::GeneticDrift object Returns : an instance of Bio::PopGen::Simulation::GeneticDrift Args : -popsize => starting N -haploid => boolean if we should simulate haploids -alleles => arrayref of the allele names OR -population => L<Bio::PopGen::PopulationI> object to initialize from some previously defined Population object (or result from a previous simulation)

next_generation
Title : next_generation Usage : my %generation = $sim->next_generation Function: Get the next generation of allele frequencies based on the current generation Returns : Hash of allele frequencies Args : 'allelefreqs' or 'population' to get back a hash of allele frequencies (default) OR a L<Bio::PopGen::Population> object

population_size
Title : population_size Usage : $obj->population_size($newval) Function: Example : Returns : value of population_size (a scalar) Args : on set, new value (a scalar or undef, optional)

set_Frequencies_Equivalent
Title : set_Frequencies_Equivalent Usage : $sim->set_Frequencies_Equivalent Function: Reset the allele frequencies so they are all even Returns : none Args : none

get_Allele_Frequencies
Title : get_Allele_Frequencies Usage : my %allele_freqs = $marker->get_Allele_Frequencies; Function: Get the alleles and their frequency (set relative to a given population - you may want to create different markers with the same name for different populations with this current implementation Returns : Associative array where keys are the names of the alleles Args : none

add_Allele_Frequency
Title : add_Allele_Frequency Usage : $marker->add_Allele_Frequency($allele,$freq) Function: Adds an allele frequency Returns : None Args : $allele - allele name $freq - frequency value

reset_alleles
Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None

validate_Frequencies
Title : validate_Frequencies Usage : if( $sim->validate_Frequencies) {} Function: Sanity checker that allele frequencies sum to 1 or less Returns : boolean Args : -strict => 1 boolean if you want to insure that sum of freqs is 1