Command-line options¶

Command line interface for stdgrimmsim - German folklore population genetic simulations.

usage: stdgrimmsim [-h] [-V] [-v | -q] [-c CACHE_DIR] [-e {msprime,slim}]
                   [--msprime-model {hudson,dtwf,smc,smc_prime}]
                   [--msprime-change-model T MODEL] [--slim-path PATH]
                   [--slim-script] [--slim-scaling-factor Q]
                   [--slim-burn-in X]
                   {AlpNac,AscPut,BasRex,BerAlp,BreSta,DraFeu,ErlKoe,FeeFlu,FraHol,HeiCol,HexWal,JotRie,KobHau,LinDra,LorRhe,MasLak,MooBay,MueGei,NixRhe,OstBal,PomBal,PukPru,RueHar,RumSti,SaxErz,SchWar,SieRab,ValKri,WerWol,WilJae,WolBay,ZweBerg,download-genetic-maps}
                   ...

Positional Arguments¶

subcommand: Possible choices: AlpNac, AscPut, BasRex, BerAlp, BreSta, DraFeu, ErlKoe, FeeFlu, FraHol, HeiCol, HexWal, JotRie, KobHau, LinDra, LorRhe, MasLak, MooBay, MueGei, NixRhe, OstBal, PomBal, PukPru, RueHar, RumSti, SaxErz, SchWar, SieRab, ValKri, WerWol, WilJae, WolBay, ZweBerg, download-genetic-maps

Named Arguments¶

-V, --version

show program’s version number and exit

-v, --verbose

Increase logging verbosity (can use be used multiple times).

Default: 1

-q, --quiet

Do not write any non-essential messages

-c, --cache-dir

Set the cache directory to the specified value. Note that this can also be set using the environment variable STDPOPSIM_CACHE. If both the environment variable and this option are set, the option takes precedence. Default: /home/docs/.cache/stdgrimmsim

-e, --engine

Possible choices: msprime, slim

Specify a simulation engine.

Default: 'msprime'

msprime specific parameters¶

--msprime-model

Possible choices: hudson, dtwf, smc, smc_prime

Specify the simulation model used by msprime. See msprime API documentation for details.

Default: 'hudson'

--msprime-change-model

Change to the specified simulation MODEL at generation T. This option may provided multiple times.

Default: []

SLiM specific parameters¶

--slim-path

Full path to `slim’ executable.

--slim-script

Write script to stdout and exit without running SLiM.

Default: False

--slim-scaling-factor

Rescale model parameters by Q to speed up simulation. See SLiM manual: 5.5 Rescaling population sizes to improve simulation performance. [default=1].

Default: 1

--slim-burn-in

Length of the burn-in phase, in units of N generations [default=10].

Default: 10

Sub-commands¶

AlpNac¶

Run simulations for Alpus nocturnalis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Alpus nocturnalis: Generation time: 10 Population size: 150000 Mutation rate: 2.601e-08 Recombination rate: 2.699e-08

stdgrimmsim AlpNac [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, nocturnal_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, nocturnal_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: SwabianAlp_1D12, SwabianSaxon_2D12, ThreeAlpRegions_3D12, NightmareExpansion_1D12, SwabianSaxonIM_2D12, FourAlpRegions_4D12, SleepParalysis_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SwabianAlp_1D12, SwabianSaxon_2D12, ThreeAlpRegions_3D12, NightmareExpansion_1D12, SwabianSaxonIM_2D12, FourAlpRegions_4D12, SleepParalysis_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

AscPut¶

Run simulations for Aschenputtel doves using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Aschenputtel doves: Generation time: 8 Population size: 420000 Mutation rate: 2.501e-08 Recombination rate: 2.6e-08

stdgrimmsim AscPut [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, hearth_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, hearth_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Hearth_1D12, HearthHazelTree_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Hearth_1D12, HearthHazelTree_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

BasRex¶

Run simulations for Basiliscus rex using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Basiliscus rex: Generation time: 80 Population size: 5000 Mutation rate: 2.001e-08 Recombination rate: 2.2e-08

stdgrimmsim BasRex [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, serpentine_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, serpentine_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: CologneDen_1D12, CologneVienna_2D12, PetrifyingGaze_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: CologneDen_1D12, CologneVienna_2D12, PetrifyingGaze_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

BerAlp¶

Run simulations for Berchta alpina using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Berchta alpina: Generation time: 35 Population size: 42000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim BerAlp [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, winter_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, winter_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BavarianAlps_1D12, BavarianAlpsSalzburg_2D12, BavarianAlpsTyrol_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BavarianAlps_1D12, BavarianAlpsSalzburg_2D12, BavarianAlpsTyrol_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

BreSta¶

Run simulations for Bremer stadtmusikanten using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Bremer stadtmusikanten: Generation time: 14 Population size: 88000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim BreSta [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, bremen_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, bremen_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Bremen_1D12, BremenLowerSaxony_2D12, BremenLowerSaxonyLuneburg_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Bremen_1D12, BremenLowerSaxony_2D12, BremenLowerSaxonyLuneburg_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DraFeu¶

Run simulations for Draco feuerspeiensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Draco feuerspeiensis: Generation time: 50 Population size: 8000 Mutation rate: 1.5e-08 Recombination rate: 1.8e-08

stdgrimmsim DraFeu [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, draconic_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, draconic_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: CastleLair_1D12, RhineBavaria_2D12, DragonSlayer_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: CastleLair_1D12, RhineBavaria_2D12, DragonSlayer_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ErlKoe¶

Run simulations for Erlkoenig sylvestris using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Erlkoenig sylvestris: Generation time: 45 Population size: 30000 Mutation rate: 2.501e-08 Recombination rate: 2.6e-08

stdgrimmsim ErlKoe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, alder_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, alder_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Thuringian_1D12, ThuringianBaltic_2D12, ThreeForestRealms_3D12, DeforestationDecline_1D12, ThuringianBalticIM_2D12, FourForestDomains_4D12, AncientWoodland_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Thuringian_1D12, ThuringianBaltic_2D12, ThreeForestRealms_3D12, DeforestationDecline_1D12, ThuringianBalticIM_2D12, FourForestDomains_4D12, AncientWoodland_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

FeeFlu¶

Run simulations for Flussfee aquaticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Flussfee aquaticus: Generation time: 30 Population size: 55000 Mutation rate: 2.701e-08 Recombination rate: 2.899e-08

stdgrimmsim FeeFlu [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, aquatic_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, aquatic_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: MainRiver_1D12, MainMoselle_2D12, ThreeTributaries_3D12, RiverPollution_1D12, MainMoselleIM_2D12, FourTributaries_4D12, SpringFlood_1D12, FairyRingExpansion_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MainRiver_1D12, MainMoselle_2D12, ThreeTributaries_3D12, RiverPollution_1D12, MainMoselleIM_2D12, FourTributaries_4D12, SpringFlood_1D12, FairyRingExpansion_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

FraHol¶

Run simulations for Holle hesseensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Holle hesseensis: Generation time: 30 Population size: 60000 Mutation rate: 2.501e-08 Recombination rate: 2.6e-08

stdgrimmsim FraHol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, well_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, well_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: WellRealm_1D12, WellSnow_2D12, ThreeRealms_3D12, WellRealmExpansion_1D12, WellSnowIM_2D12, FourRealms_4D12, GoldenAge_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: WellRealm_1D12, WellSnow_2D12, ThreeRealms_3D12, WellRealmExpansion_1D12, WellSnowIM_2D12, FourRealms_4D12, GoldenAge_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HeiCol¶

Run simulations for Heinzelmaennchen coloniensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.

Default population parameters for Heinzelmaennchen coloniensis: Generation time: 8 Population size: 300000 Mutation rate: 3.002e-08 Recombination rate: 3.199e-08

stdgrimmsim HeiCol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, workshop_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, workshop_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Cologne_1D12, CologneAachen_2D12, ThreeRhinelandCities_3D12, TailorsWifeBottleneck_1D12, CologneAachenIM_2D12, FourRhinelandCities_4D12, NocturnalWorkshop_1D12, CologneExpansion_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Cologne_1D12, CologneAachen_2D12, ThreeRhinelandCities_3D12, TailorsWifeBottleneck_1D12, CologneAachenIM_2D12, FourRhinelandCities_4D12, NocturnalWorkshop_1D12, CologneExpansion_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HexWal¶

Run simulations for Hexara walpurgis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Hexara walpurgis: Generation time: 30 Population size: 25000 Mutation rate: 2.301e-08 Recombination rate: 2.499e-08

stdgrimmsim HexWal [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, hexen_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, hexen_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BrockenSabbath_1D12, BrockenBamberg_2D12, WitchTrialPurge_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BrockenSabbath_1D12, BrockenBamberg_2D12, WitchTrialPurge_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

JotRie¶

Run simulations for Jotunnus riesensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Jotunnus riesensis: Generation time: 150 Population size: 3000 Mutation rate: 1e-08 Recombination rate: 1.2e-08

stdgrimmsim JotRie [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, jotun_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, jotun_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: NiflheimClan_1D12, NiflJotun_2D12, Ragnarok_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: NiflheimClan_1D12, NiflJotun_2D12, Ragnarok_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

KobHau¶

Run simulations for Koboldus domesticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Koboldus domesticus: Generation time: 15 Population size: 200000 Mutation rate: 2.802e-08 Recombination rate: 2.999e-08

stdgrimmsim KobHau [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, hearth_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, hearth_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: UrbanKobold_1D12, UrbanRural_2D12, ThreeKoboldTypes_3D12, MedievalUrbanBoom_1D12, UrbanRuralIM_2D12, FourKoboldNiches_4D12, IndustrialDecline_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: UrbanKobold_1D12, UrbanRural_2D12, ThreeKoboldTypes_3D12, MedievalUrbanBoom_1D12, UrbanRuralIM_2D12, FourKoboldNiches_4D12, IndustrialDecline_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

LinDra¶

Run simulations for Lindwurm draconicus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Lindwurm draconicus: Generation time: 200 Population size: 2000 Mutation rate: 1.8e-08 Recombination rate: 2e-08

stdgrimmsim LinDra [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, draconic_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, draconic_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: RhineDragon_1D12, RhineKlagenfurt_2D12, ThreeDragonLairs_3D12, DragonSlayerBottleneck_1D12, RhineKlagenfurtIM_2D12, FourDragonLairs_4D12, NearExtinction_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: RhineDragon_1D12, RhineKlagenfurt_2D12, ThreeDragonLairs_3D12, DragonSlayerBottleneck_1D12, RhineKlagenfurtIM_2D12, FourDragonLairs_4D12, NearExtinction_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

LorRhe¶

Run simulations for Loreley rhenanus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Loreley rhenanus: Generation time: 40 Population size: 35000 Mutation rate: 2.501e-08 Recombination rate: 2.7e-08

stdgrimmsim LorRhe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, rock_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, rock_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: LoreleyRock_1D12, LoreleyMiddleRhine_2D12, RhineGorge_3D12, LoreleyDecline_1D12, LoreleyMiddleRhineIM_2D12, FourRhineStretches_4D12, SirenSong_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: LoreleyRock_1D12, LoreleyMiddleRhine_2D12, RhineGorge_3D12, LoreleyDecline_1D12, LoreleyMiddleRhineIM_2D12, FourRhineStretches_4D12, SirenSong_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

MasLak¶

Run simulations for Masurius lacustris using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Masurius lacustris: Generation time: 48 Population size: 32000 Mutation rate: 2.601e-08 Recombination rate: 2.6e-08

stdgrimmsim MasLak [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, lake_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, lake_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: MasurianLakes_1D12, MasurianLakesSpirdingsee_2D12, MasurianThreeLakes_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MasurianLakes_1D12, MasurianLakesSpirdingsee_2D12, MasurianThreeLakes_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

MooBay¶

Run simulations for Moosweib bavaricum using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Moosweib bavaricum: Generation time: 28 Population size: 38000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim MooBay [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, forest_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, forest_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BayrischerWald_1D12, BayrischerWaldOberpfalz_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BayrischerWald_1D12, BayrischerWaldOberpfalz_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

MueGei¶

Run simulations for Muellerin geisterhaft using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Muellerin geisterhaft: Generation time: 20 Population size: 40000 Mutation rate: 2.802e-08 Recombination rate: 2.999e-08

stdgrimmsim MueGei [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, spectral_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, spectral_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BlackForestMill_1D12, ForestMarsh_2D12, IndustrialDecline_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BlackForestMill_1D12, ForestMarsh_2D12, IndustrialDecline_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

NixRhe¶

Run simulations for Nixus rhenanus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Nixus rhenanus: Generation time: 50 Population size: 45000 Mutation rate: 2.601e-08 Recombination rate: 2.8e-08

stdgrimmsim NixRhe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, river_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, river_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Rhine_1D12, RhineElbe_2D12, ThreeRivers_3D12, RhineBottleneck_1D12, RhineElbeIM_2D12, FourRivers_4D12, TidalFluctuation_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Rhine_1D12, RhineElbe_2D12, ThreeRivers_3D12, RhineBottleneck_1D12, RhineElbeIM_2D12, FourRivers_4D12, TidalFluctuation_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

OstBal¶

Run simulations for Ostpreussius balticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Ostpreussius balticus: Generation time: 55 Population size: 28000 Mutation rate: 2.601e-08 Recombination rate: 2.7e-08

stdgrimmsim OstBal [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, baltic_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, baltic_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: KurischeNehrung_1D12, KurischeNehrungMemelland_2D12, EastPrussiaBaltic_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: KurischeNehrung_1D12, KurischeNehrungMemelland_2D12, EastPrussiaBaltic_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

PomBal¶

Run simulations for Pommersch balticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Pommersch balticus: Generation time: 52 Population size: 36000 Mutation rate: 2.601e-08 Recombination rate: 2.7e-08

stdgrimmsim PomBal [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, coast_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, coast_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Usedom_1D12, UsedomRugen_2D12, PomeraniaBaltic_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Usedom_1D12, UsedomRugen_2D12, PomeraniaBaltic_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

PukPru¶

Run simulations for Puk prussicus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.

Default population parameters for Puk prussicus: Generation time: 18 Population size: 180000 Mutation rate: 2.601e-08 Recombination rate: 2.6e-08

stdgrimmsim PukPru [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, house_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, house_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: EastPrussia_1D12, EastPrussiaWestPrussia_2D12, EastPrussiaBerlinBrandenburg_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: EastPrussia_1D12, EastPrussiaWestPrussia_2D12, EastPrussiaBerlinBrandenburg_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

RueHar¶

Run simulations for Ruebezahl harzensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Ruebezahl harzensis: Generation time: 100 Population size: 15000 Mutation rate: 2.201e-08 Recombination rate: 2.4e-08

stdgrimmsim RueHar [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, mountain_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, mountain_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Riesengebirge_1D12, HarzRiesengebirge_2D12, ThreeMountains_3D12, AncientMountainSpirit_1D12, RiesenHarzIM_2D12, FourMountainSpirits_4D12, IceAgeSurvival_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Riesengebirge_1D12, HarzRiesengebirge_2D12, ThreeMountains_3D12, AncientMountainSpirit_1D12, RiesenHarzIM_2D12, FourMountainSpirits_4D12, IceAgeSurvival_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

RumSti¶

Run simulations for Rumpelstilzchen thuringiensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.

Default population parameters for Rumpelstilzchen thuringiensis: Generation time: 22 Population size: 48000 Mutation rate: 2.501e-08 Recombination rate: 2.6e-08

stdgrimmsim RumSti [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, mill_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, mill_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Thuringia_1D12, ThuringiaHesse_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Thuringia_1D12, ThuringiaHesse_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SaxErz¶

Run simulations for Bergmann erzgebirgensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Bergmann erzgebirgensis: Generation time: 28 Population size: 72000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim SaxErz [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, mine_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, mine_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Erzgebirge_1D12, ErzgebirgeVogtland_2D12, ErzgebirgeVogtlandDresden_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Erzgebirge_1D12, ErzgebirgeVogtland_2D12, ErzgebirgeVogtlandDresden_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SchWar¶

Run simulations for Silvani schwarzwaldensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Silvani schwarzwaldensis: Generation time: 20 Population size: 120000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim SchWar [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, forest_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, forest_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BlackForest_1D12, NorthSouthBlackForest_2D12, ThreeForestZones_3D12, ForestExpansion_1D12, NorthSouthIM_2D12, FourForestValleys_4D12, DeforestationRecovery_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BlackForest_1D12, NorthSouthBlackForest_2D12, ThreeForestZones_3D12, ForestExpansion_1D12, NorthSouthIM_2D12, FourForestValleys_4D12, DeforestationRecovery_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SieRab¶

Run simulations for Corvus septem ravens using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Corvus septem ravens: Generation time: 18 Population size: 65000 Mutation rate: 2.601e-08 Recombination rate: 2.7e-08

stdgrimmsim SieRab [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, glass_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, glass_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: GlassMountain_1D12, GlassMountainForestWell_2D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: GlassMountain_1D12, GlassMountainForestWell_2D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ValKri¶

Run simulations for Valkyria kriegensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Valkyria kriegensis: Generation time: 100 Population size: 12000 Mutation rate: 2.201e-08 Recombination rate: 2.4e-08

stdgrimmsim ValKri [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, valkyrja_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, valkyrja_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ValhallaHost_1D12, ValhallaMidgard_2D12, Christianization_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ValhallaHost_1D12, ValhallaMidgard_2D12, Christianization_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

WerWol¶

Run simulations for Werwolfus lupinus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Werwolfus lupinus: Generation time: 20 Population size: 10000 Mutation rate: 2.3e-08 Recombination rate: 2.4e-08

stdgrimmsim WerWol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, lupine_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, lupine_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: Rhineland_1D12, RhinelandLivonian_2D12, ThreeWerewolfPacks_3D12, WitchTrialBottleneck_1D12, RhinelandLivonianIM_2D12, FourWerewolfPacks_4D12, LycanthropeRecovery_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Rhineland_1D12, RhinelandLivonian_2D12, ThreeWerewolfPacks_3D12, WitchTrialBottleneck_1D12, RhinelandLivonianIM_2D12, FourWerewolfPacks_4D12, LycanthropeRecovery_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

WilJae¶

Run simulations for Wildjaeger germanicus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Wildjaeger germanicus: Generation time: 60 Population size: 25000 Mutation rate: 2.401e-08 Recombination rate: 2.3e-08

stdgrimmsim WilJae [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, spectral_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, spectral_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: NorthernHunt_1D12, NorthSouthHunt_2D12, ThreeHuntHosts_3D12, ChristianizationBottleneck_1D12, NorthSouthHuntIM_2D12, FourHuntRegions_4D12, WinterSolstice_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: NorthernHunt_1D12, NorthSouthHunt_2D12, ThreeHuntHosts_3D12, ChristianizationBottleneck_1D12, NorthSouthHuntIM_2D12, FourHuntRegions_4D12, WinterSolstice_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

WolBay¶

Run simulations for Wolpertingerus bavarius using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Wolpertingerus bavarius: Generation time: 12 Population size: 95000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim WolBay [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                   [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                   [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                   [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                   [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                   samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, alpine_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, alpine_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: UpperBavaria_1D12, UpperBavariaBavarianForest_2D12, BavariaThreeRegion_3D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: UpperBavaria_1D12, UpperBavariaBavarianForest_2D12, BavariaThreeRegion_3D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ZweBerg¶

Run simulations for Zwergus bergensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Zwergus bergensis: Generation time: 25 Population size: 80000 Mutation rate: 2.501e-08 Recombination rate: 2.5e-08

stdgrimmsim ZweBerg [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                    [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                    [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                    [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                    [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                    samples [samples ...]

Positional Arguments¶

samples: The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments¶

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, mountain_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, mountain_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: BlackForest_1D12, HarzBlackForest_2D12, AlpineDwarfRadiation_3D12, MineCollapse_1D12, IsolationMigration_2D12, FourMountainRanges_4D12, PostGlacialExpansion_1D12

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BlackForest_1D12, HarzBlackForest_2D12, AlpineDwarfRadiation_3D12, MineCollapse_1D12, IsolationMigration_2D12, FourMountainRanges_4D12, PostGlacialExpansion_1D12. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

--dfe-bed-file

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

download-genetic-maps¶

Download genetic maps and store them in the cache directory. Maps are downloaded regardless of whether they are already in the cache or not. Please use the –cache-dir option to download maps to a specific directory.

stdgrimmsim download-genetic-maps [-h] [species] [genetic_maps ...]

Positional Arguments¶

species: Download genetic maps for this species. If not specified download all known genetic maps.
genetic_maps: If specified, download these genetic maps. If no maps are provided, download all maps for this species.