Index

_

__init__() (quantgen.core.chromosome.chromosome method) (quantgen.core.diploidIndividual.diploidIndividual method) (quantgen.core.haplotype.haplotype method) (quantgen.core.locus.locus method) (quantgen.sim.SLiM_writer.SLiM_generator method)

A

add_chromosome_element() (quantgen.sim.SLiM_writer.SLiM_generator method) add_element_type() (quantgen.sim.SLiM_writer.SLiM_generator method) add_initialization_file() (quantgen.sim.SLiM_writer.SLiM_generator method) add_interval_recomb_rate() (quantgen.sim.SLiM_writer.SLiM_generator method) add_locus() (quantgen.core.chromosome.chromosome method)

add_mutation_type() (quantgen.sim.SLiM_writer.SLiM_generator method) add_output_option() (quantgen.sim.SLiM_writer.SLiM_generator method) add_population() (quantgen.sim.SLiM_writer.SLiM_generator method) add_predetermined_mutation() (quantgen.sim.SLiM_writer.SLiM_generator method)

C

change_pop_migration() (quantgen.sim.SLiM_writer.SLiM_generator method) change_pop_selfing() (quantgen.sim.SLiM_writer.SLiM_generator method) change_pop_size() (quantgen.sim.SLiM_writer.SLiM_generator method)

chrom_length (quantgen.sim.SLiM_writer.SLiM_generator attribute) chromosome (class in quantgen.core.chromosome) chromosomeTest (class in quantgen.test.core.chromosomeTest)

D

diploidIndividual (class in quantgen.core.diploidIndividual)

diploidIndividualTest (class in quantgen.test.core.diploidIndividualTest)

E

element_types (quantgen.sim.SLiM_writer.SLiM_generator attribute)

elements (quantgen.sim.SLiM_writer.SLiM_generator attribute)

G

gene_conversion_settings (quantgen.sim.SLiM_writer.SLiM_generator attribute) generations (quantgen.sim.SLiM_writer.SLiM_generator attribute) get_a_d_values() (quantgen.core.locus.locus method) get_alpha() (quantgen.core.locus.locus method) get_alpha_vals() (quantgen.core.locus.locus method) get_bordering_loci() (quantgen.core.chromosome.chromosome method) get_bordering_loci_inds() (quantgen.core.chromosome.chromosome method) get_chrom_length() (quantgen.core.chromosome.chromosome method)

get_locus() (quantgen.core.chromosome.chromosome method) get_locus_by_name() (quantgen.core.chromosome.chromosome method) get_locus_ind() (quantgen.core.chromosome.chromosome method) get_mu_G() (quantgen.core.locus.locus method) get_raw_G() (quantgen.core.locus.locus method) get_raw_nonepistatic_G() (quantgen.core.diploidIndividual.diploidIndividual method) get_recomb_points() (quantgen.core.chromosome.chromosome method)

H

haplotype (class in quantgen.core.haplotype)

haplotypeTest (class in quantgen.test.core.haplotypeTest)

I

individual (class in quantgen.core.diploidIndividual)

initialization_file (quantgen.sim.SLiM_writer.SLiM_generator attribute)

L

locus (class in quantgen.core.locus)

locusTest (class in quantgen.test.core.locusTest)

M

mate() (quantgen.core.diploidIndividual.diploidIndividual method) mu (quantgen.sim.SLiM_writer.SLiM_generator attribute)

mutation_types (quantgen.sim.SLiM_writer.SLiM_generator attribute)

O

output_settings (quantgen.sim.SLiM_writer.SLiM_generator attribute)

P

populations (quantgen.sim.SLiM_writer.SLiM_generator attribute)

predetermined_mutations (quantgen.sim.SLiM_writer.SLiM_generator attribute)

Q

quantgen (module) quantgen.core (module) quantgen.core.chromosome (module) quantgen.core.diploidIndividual (module) quantgen.core.haplotype (module) quantgen.core.locus (module) quantgen.sim (module)

quantgen.sim.SLiM_writer (module) quantgen.test (module) quantgen.test.core (module) quantgen.test.core.chromosomeTest (module) quantgen.test.core.diploidIndividualTest (module) quantgen.test.core.haplotypeTest (module) quantgen.test.core.locusTest (module)

R

recomb_rates (quantgen.sim.SLiM_writer.SLiM_generator attribute)

recombine2() (quantgen.core.haplotype.haplotype static method)

S

seed (quantgen.sim.SLiM_writer.SLiM_generator attribute) set_a() (quantgen.core.locus.locus method) set_cM() (quantgen.core.locus.locus method) set_gene_conversion() (quantgen.sim.SLiM_writer.SLiM_generator method)

set_k() (quantgen.core.locus.locus method) set_random_seed() (quantgen.sim.SLiM_writer.SLiM_generator method) setUp() (quantgen.test.core.diploidIndividualTest.diploidIndividualTest method) (quantgen.test.core.haplotypeTest.haplotypeTest method) (quantgen.test.core.locusTest.locusTest method) SLiM_generator (class in quantgen.sim.SLiM_writer)

T

test_add_locus() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_get_a_d_values() (quantgen.test.core.locusTest.locusTest method) test_get_alpha() (quantgen.test.core.locusTest.locusTest method) test_get_bordering_loci() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_get_bordering_loci_inds() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_get_chrom_length() (quantgen.test.core.chromosomeTest.chromosomeTest method)

test_get_locus() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_get_locus_by_name() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_get_raw_G() (quantgen.test.core.locusTest.locusTest method) test_get_raw_nonepistatic_G() (quantgen.test.core.diploidIndividualTest.diploidIndividualTest method) test_recomb_points() (quantgen.test.core.chromosomeTest.chromosomeTest method) test_recombine2() (quantgen.test.core.haplotypeTest.haplotypeTest method)

W

write_input_file() (quantgen.sim.SLiM_writer.SLiM_generator method)