Class Loci

java.lang.Object
  Loci

public class Loci

extends java.lang.Object

The source code for these objects is available upon request from Alistair Blachford ( alistair@zoology.ubc.ca ).

Loci reads the command-line run parameters, creates an instance of Deme and acts as metronome for the run.

Usage:

java -jar Loci.jar maxGen k nAttribs delMutRate benMutRate minRecRate modRecRate selRate epistasis assort initq

maxGen

maximum number of generations to run

k

the population size to use

nAttribs

the number of loci on a chromosome. Limitations on number are determined by class Bion

delMutRate

per locus forward (deleterious) mutation rate

benMutRate

per locus backward (beneficial) mutation rate

minRecRate

the minimum recombination rate between loci. Presence of mutation modifier alleles will elevate this.

modRecRate

the amount by which recombination rate is increased in an individual homozygous for the modifier

selRate

selection coefficient. Exact meaning depends on fitness function being used

epistasis

carefully peer at fitness function to see what this is. It warps the effects of increasing number of deleterious alleles.

assort

assortativeness of mating by fitness (not by genotype)

initq

the initial frequency of deleterious alleles across all fitness loci. Used only to create all individuals at time 0.

Output:

Except for usage errors, all output is from class Deme.

Sample Run:

java -jar Loci.jar 5 10000 64 .001 0 .01 0 .01 0 0 .5
1 -0.00188 -0.00753 0.50275 0.53361 0.01567 0.49972 1226 0 12695 84 0.52683 0
2 0.00032 0.00128 0.50030 0.53492 -0.00827 0.49780 1290 0 12544 83 0.50059 1
3 -0.00219 -0.00876 0.50090 0.53583 -0.00322 0.49645 1213 0 12581 84 0.49866 0
4 -0.00066 -0.00263 0.50610 0.53752 -0.00799 0.49393 1257 0 12667 81 0.49858 0
5 -0.00395 -0.01582 0.50800 0.53887 0.00304 0.49193 1276 0 12561 81 0.51757 1
Output fields are described in class Deme.

Constructor Summary

Loci()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Loci

public Loci()

Method Detail

main

public static void main(java.lang.String[] args)