Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W A add_admixture() (msprime.Demography method) add_census() (msprime.Demography method) add_individual() (msprime.PedigreeBuilder method) add_instantaneous_bottleneck() (msprime.Demography method) add_mass_migration() (msprime.Demography method) add_migration_rate_change() (msprime.Demography method) add_population() (msprime.Demography method) add_population_parameters_change() (msprime.Demography method) add_population_split() (msprime.Demography method) add_simple_bottleneck() (msprime.Demography method) add_symmetric_migration_rate_change() (msprime.Demography method) AncestryModel (class in msprime) assert_equal() (msprime.Demography method) B BetaCoalescent (class in msprime) BinaryMutationModel (class in msprime) BLOSUM62 (class in msprime) C CENSUS (msprime.NodeType attribute) CensusEvent (class in msprime) coalescence_rate_trajectory() (msprime.DemographyDebugger method) COMMON_ANCESTOR (msprime.NodeType attribute) copy() (msprime.Demography method) (msprime.RateMap method) D Debian/Ubuntu debug() (msprime.Demography method) default_sampling_time (msprime.Population attribute) Demography (class in msprime) DemographyDebugger (class in msprime) description (msprime.Population attribute) DiracCoalescent (class in msprime) DiscreteTimeWrightFisher (class in msprime) duration (msprime.AncestryModel attribute) E EL2 (class in msprime) epoch_start_time (msprime.DemographyDebugger property) extra_metadata (msprime.Population attribute) F F84 (class in msprime) finalise() (msprime.PedigreeBuilder method) find_index() (msprime.RateMap method) FixedPedigree (class in msprime) FreeBSD from_demes() (msprime.Demography static method) from_old_style() (msprime.Demography static method) from_species_tree() (msprime.Demography static method) from_starbeast() (msprime.Demography static method) from_tree_sequence() (msprime.Demography static method) G GENE_CONVERSION (msprime.NodeType attribute) get_cumulative_mass() (msprime.RateMap method) get_rate() (msprime.RateMap method) get_total_recombination_rate() (msprime.RecombinationMap method) growth_rate (msprime.Population attribute) GTR (class in msprime) H HKY (class in msprime) I id (msprime.Population attribute) InfiniteAlleles (class in msprime) InfiniteSites (class in msprime) initial_size (msprime.Population attribute) initially_active (msprime.Population attribute) is_equivalent() (msprime.Demography method) island_model() (msprime.Demography static method) isolated_model() (msprime.Demography static method) J JC69 (class in msprime) L left (msprime.RateMap property) lineage_probabilities() (msprime.DemographyDebugger method) log_arg_likelihood() (in module msprime) log_mutation_likelihood() (in module msprime) M mass (msprime.RateMap property) MassMigration (class in msprime) MatrixMutationModel (class in msprime) mean_coalescence_time() (msprime.DemographyDebugger method) mean_rate (msprime.RateMap property) mean_recombination_rate (msprime.RecombinationMap property) MicrosatMutationModel (class in msprime) mid (msprime.RateMap property) MIGRANT (msprime.NodeType attribute) MigrationRateChange (class in msprime) missing (msprime.RateMap property) missing_intervals() (msprime.RateMap method) msprime.NODE_IS_CA_EVENT (in module msprime) msprime.NODE_IS_CEN_EVENT (in module msprime) msprime.NODE_IS_GC_EVENT (in module msprime) msprime.NODE_IS_MIG_EVENT (in module msprime) msprime.NODE_IS_PASS_THROUGH (in module msprime) msprime.NODE_IS_RE_EVENT (in module msprime) mutate() (in module msprime) MutationModel (class in msprime) N name (msprime.Population attribute) NodeType (class in msprime) non_missing (msprime.RateMap property) num_epochs (msprime.DemographyDebugger property) num_intervals (msprime.RateMap property) num_missing_intervals (msprime.RateMap property) num_non_missing_intervals (msprime.RateMap property) num_samples (msprime.SampleSet attribute) O OS X P PAM (class in msprime) parse_pedigree() (in module msprime) PASS_THROUGH (msprime.NodeType attribute) PedigreeBuilder (class in msprime) ploidy (msprime.SampleSet attribute) Population (class in msprime) population (msprime.SampleSet attribute) population_size_history (msprime.DemographyDebugger property) population_size_trajectory() (msprime.DemographyDebugger method) PopulationConfiguration (class in msprime) PopulationParametersChange (class in msprime) position (msprime.RateMap property) possible_lineage_locations() (msprime.DemographyDebugger method) print_history() (msprime.DemographyDebugger method) R rate (msprime.RateMap property) RateMap (class in msprime) read_hapmap() (msprime.RateMap static method) (msprime.RecombinationMap class method) RECOMBINANT (msprime.NodeType attribute) RecombinationMap (class in msprime) Redhat/Fedora right (msprime.RateMap property) S Sample (class in msprime) SampleSet (class in msprime) sequence_length (msprime.RateMap property) set_migration_rate() (msprime.Demography method) set_symmetric_migration_rate() (msprime.Demography method) sim_ancestry() (in module msprime) sim_mutations() (in module msprime) simulate() (in module msprime) SimulationModelChange (class in msprime) slice() (msprime.RateMap method) SLiMMutationModel (class in msprime) SmcApproxCoalescent (class in msprime) SmcPrimeApproxCoalescent (class in msprime) SMM (class in msprime) span (msprime.RateMap property) StandardCoalescent (class in msprime) stepping_stone_model() (msprime.Demography static method) SweepGenicSelection (class in msprime) T time (msprime.SampleSet attribute) to_demes() (msprime.Demography method) total_mass (msprime.RateMap property) TPM (class in msprime) U uniform() (msprime.RateMap static method) uniform_map() (msprime.RecombinationMap class method) V validate() (msprime.Demography method) W Windows
