Command-line options¶

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

usage: stdferdowsim [-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]
                    {AfrHor,AlDem,AzhDra,BahFir,ChaGri,DaeWar,DivMaz,DouGia,DraAng,EsfSmi,FarGlo,GavPri,GhoUnd,GulRos,HumBir,JamPis,KayDyn,KhiWis,ManTig,MarMor,MitSol,NarHer,PahDiv,PerPar,PriJin,RakEqu,RosHer,RudSim,SenBir,ShaSha,SimAvi,SorWiz,TurNom,YazGua,ZalAlb,ZorPri,download-genetic-maps}
                    ...

Positional Arguments¶

subcommand: Possible choices: AfrHor, AlDem, AzhDra, BahFir, ChaGri, DaeWar, DivMaz, DouGia, DraAng, EsfSmi, FarGlo, GavPri, GhoUnd, GulRos, HumBir, JamPis, KayDyn, KhiWis, ManTig, MarMor, MitSol, NarHer, PahDiv, PerPar, PriJin, RakEqu, RosHer, RudSim, SenBir, ShaSha, SimAvi, SorWiz, TurNom, YazGua, ZalAlb, ZorPri, 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/stdferdowsim

-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¶

AfrHor¶

Run simulations for Afrasiyab horrens 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 Afrasiyab horrens: Generation time: 28 Population size: 65000 Mutation rate: 2.801e-08 Recombination rate: 2.2e-08

stdferdowsim AfrHor [-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, afrasiyab_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, afrasiyab_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10. 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

AlDem¶

Run simulations for Al daemonius 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 Al daemonius: Generation time: 20 Population size: 70000 Mutation rate: 6.003e-08 Recombination rate: 2e-08

stdferdowsim AlDem [-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, al_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, al_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

AzhDra¶

Run simulations for Azhdaha draconius 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 Azhdaha draconius: Generation time: 500 Population size: 5000 Mutation rate: 5.002e-09 Recombination rate: 2.999e-08

stdferdowsim AzhDra [-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, damavand_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, damavand_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

BahFir¶

Run simulations for Bahram firesteed 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 Bahram firesteed: Generation time: 30 Population size: 35000 Mutation rate: 2.801e-08 Recombination rate: 3.199e-08

stdferdowsim BahFir [-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, bahram_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, bahram_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

ChaGri¶

Run simulations for Chamrosh griffinus 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 Chamrosh griffinus: Generation time: 40 Population size: 7000 Mutation rate: 1.501e-08 Recombination rate: 5.499e-08

stdferdowsim ChaGri [-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, chamrosh_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, chamrosh_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

DaeWar¶

Run simulations for Daeva warrior 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 Daeva warrior: Generation time: 50 Population size: 90000 Mutation rate: 3.501e-08 Recombination rate: 2e-08

stdferdowsim DaeWar [-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, daeva_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, daeva_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

DivMaz¶

Run simulations for Divus mazandarensis 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 Divus mazandarensis: Generation time: 80 Population size: 50000 Mutation rate: 3.001e-08 Recombination rate: 2e-08

stdferdowsim DivMaz [-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, mazand_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, mazand_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

DouGia¶

Run simulations for Dough giant 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 Dough giant: Generation time: 120 Population size: 4000 Mutation rate: 8.003e-09 Recombination rate: 1.5e-08

stdferdowsim DouGia [-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, sepid_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, sepid_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

DraAng¶

Run simulations for Druj angra 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 Druj angra: Generation time: 25 Population size: 150000 Mutation rate: 5.002e-08 Recombination rate: 1.5e-08

stdferdowsim DraAng [-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, druj_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, druj_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

EsfSmi¶

Run simulations for Esfandiyar smithius 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 Esfandiyar smithius: Generation time: 30 Population size: 32000 Mutation rate: 2.001e-08 Recombination rate: 2.499e-08

stdferdowsim EsfSmi [-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, rouyin_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, rouyin_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

FarGlo¶

Run simulations for Faravahar glorius 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 Faravahar glorius: Generation time: 60 Population size: 80000 Mutation rate: 1e-08 Recombination rate: 6.999e-08

stdferdowsim FarGlo [-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, fravashi_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, fravashi_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

GavPri¶

Run simulations for Gavaevodata primus 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 Gavaevodata primus: Generation time: 300 Population size: 2000 Mutation rate: 3.001e-09 Recombination rate: 2e-08

stdferdowsim GavPri [-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, primal_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, primal_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

GhoUnd¶

Run simulations for Ghoul underworld 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 Ghoul underworld: Generation time: 25 Population size: 40000 Mutation rate: 4.502e-08 Recombination rate: 1.8e-08

stdferdowsim GhoUnd [-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, ghul_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, ghul_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

GulRos¶

Run simulations for Gulistan rosagarden 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 Gulistan rosagarden: Generation time: 20 Population size: 55000 Mutation rate: 4.002e-08 Recombination rate: 2.999e-08

stdferdowsim GulRos [-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, gulistan_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, gulistan_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

HumBir¶

Run simulations for Huma paradisica 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 Huma paradisica: Generation time: 150 Population size: 8000 Mutation rate: 1e-08 Recombination rate: 5.999e-08

stdferdowsim HumBir [-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, huma_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, huma_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

JamPis¶

Run simulations for Jamshid pishdadius 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 Jamshid pishdadius: Generation time: 100 Population size: 60000 Mutation rate: 1.501e-08 Recombination rate: 4.999e-08

stdferdowsim JamPis [-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, persepolis_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, persepolis_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

KayDyn¶

Run simulations for Kayanian dynasticus 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 Kayanian dynasticus: Generation time: 30 Population size: 45000 Mutation rate: 2.001e-08 Recombination rate: 2.999e-08

stdferdowsim KayDyn [-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, kayani_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, kayani_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

KhiWis¶

Run simulations for Khidr wisdomus 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 Khidr wisdomus: Generation time: 1000 Population size: 500 Mutation rate: 1e-09 Recombination rate: 4.999e-09

stdferdowsim KhiWis [-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, khidr_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, khidr_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

ManTig¶

Run simulations for Manticore persicus 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 Manticore persicus: Generation time: 60 Population size: 12000 Mutation rate: 2.501e-08 Recombination rate: 3.999e-08

stdferdowsim ManTig [-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, mardykhor_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, mardykhor_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

MarMor¶

Run simulations for Marduk mortalis 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 Marduk mortalis: Generation time: 45 Population size: 75000 Mutation rate: 2.001e-08 Recombination rate: 3.499e-08

stdferdowsim MarMor [-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, marduk_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, marduk_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

MitSol¶

Run simulations for Mithra solarius 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 Mithra solarius: Generation time: 800 Population size: 1000 Mutation rate: 2.001e-09 Recombination rate: 9.998e-09

stdferdowsim MitSol [-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, mithra_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, mithra_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

NarHer¶

Run simulations for Nart heronius 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 Nart heronius: Generation time: 28 Population size: 22000 Mutation rate: 2.501e-08 Recombination rate: 2.799e-08

stdferdowsim NarHer [-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, nart_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, nart_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

PahDiv¶

Run simulations for Pahlavan divanus 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 Pahlavan divanus: Generation time: 35 Population size: 28000 Mutation rate: 2.201e-08 Recombination rate: 2.999e-08

stdferdowsim PahDiv [-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, pahlavan_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, pahlavan_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

PerPar¶

Run simulations for Peri paradisi 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 Peri paradisi: Generation time: 40 Population size: 100000 Mutation rate: 4.002e-08 Recombination rate: 3.499e-08

stdferdowsim PerPar [-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, peri_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, peri_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

PriJin¶

Run simulations for Jinnus persicus 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 Jinnus persicus: Generation time: 30 Population size: 200000 Mutation rate: 5.002e-08 Recombination rate: 2.999e-08

stdferdowsim PriJin [-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, jinn_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, jinn_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

RakEqu¶

Run simulations for Rakhsh equinus 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 Rakhsh equinus: Generation time: 25 Population size: 3000 Mutation rate: 2.201e-08 Recombination rate: 1.5e-08

stdferdowsim RakEqu [-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, rakhsh_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, rakhsh_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

RosHer¶

Run simulations for Rostam heroicus 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 Rostam heroicus: Generation time: 35 Population size: 25000 Mutation rate: 2.001e-08 Recombination rate: 2.499e-08

stdferdowsim RosHer [-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, zabul_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, zabul_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

RudSim¶

Run simulations for Rudabeh simurghica 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 Rudabeh simurghica: Generation time: 30 Population size: 18000 Mutation rate: 2.201e-08 Recombination rate: 2.999e-08

stdferdowsim RudSim [-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, kabul_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, kabul_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

SenBir¶

Run simulations for Senmurv birddog 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 Senmurv birddog: Generation time: 45 Population size: 10000 Mutation rate: 2.001e-08 Recombination rate: 4.999e-08

stdferdowsim SenBir [-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, senmurv_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, senmurv_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

ShaSha¶

Run simulations for Shahbaz shahinus 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 Shahbaz shahinus: Generation time: 15 Population size: 6000 Mutation rate: 3.001e-08 Recombination rate: 5.999e-08

stdferdowsim ShaSha [-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, shahbaz_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, shahbaz_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

SimAvi¶

Run simulations for Simurgh avianus 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 Simurgh avianus: Generation time: 200 Population size: 15000 Mutation rate: 1.2e-08 Recombination rate: 7.998e-08

stdferdowsim SimAvi [-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, alborz_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, alborz_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

SorWiz¶

Run simulations for Sorcerer wizardus 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 Sorcerer wizardus: Generation time: 50 Population size: 30000 Mutation rate: 3.501e-08 Recombination rate: 2.499e-08

stdferdowsim SorWiz [-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, jadoo_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, jadoo_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

TurNom¶

Run simulations for Turanian nomadicus 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 Turanian nomadicus: Generation time: 22 Population size: 120000 Mutation rate: 3.001e-08 Recombination rate: 2e-08

stdferdowsim TurNom [-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, turan_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, turan_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

YazGua¶

Run simulations for Yazata guardian 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 Yazata guardian: Generation time: 500 Population size: 3000 Mutation rate: 5.002e-09 Recombination rate: 2e-08

stdferdowsim YazGua [-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, yazata_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, yazata_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

ZalAlb¶

Run simulations for Zal albinus 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 Zal albinus: Generation time: 35 Population size: 20000 Mutation rate: 1.801e-08 Recombination rate: 3.999e-08

stdferdowsim ZalAlb [-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, zal_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, zal_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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

ZorPri¶

Run simulations for Zoroaster primus 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 Zoroaster primus: Generation time: 100 Population size: 10000 Mutation rate: 1.2e-08 Recombination rate: 3.999e-08

stdferdowsim ZorPri [-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, zartosht_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, zartosht_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: Constant_1F10, ThreeEpoch_1F10, TwoPopSplit_2F10, GhostAdmixture_3F10, ThreePopAdmix_3F10, FourRegion_4F10, FiveRealm_5F10, SixPopExtRecolon_6F10, AsymReversal_2F10, SilkRoad_8F10

--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.

stdferdowsim 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.