Command-line options

Command line interface for stdpopsim.

usage: stdpopsim [-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]
                 {AedAeg,AnaPla,AnoCar,AnoGam,ApiMel,AraTha,BosTau,CaeEle,CanFam,ChlRei,DroMel,DroSec,EscCol,GasAcu,HelAnn,HelMel,HomSap,PanTro,PapAnu,PonAbe,StrAga,download-genetic-maps}
                 ...

Positional Arguments

subcommand

Possible choices: AedAeg, AnaPla, AnoCar, AnoGam, ApiMel, AraTha, BosTau, CaeEle, CanFam, ChlRei, DroMel, DroSec, EscCol, GasAcu, HelAnn, HelMel, HomSap, PanTro, PapAnu, PonAbe, StrAga, 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/runner/.cache/stdpopsim

-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:

AedAeg

Run simulations for Aedes aegypti 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 Aedes aegypti: Generation time: 0.06666666666666667 Population size: 1000000.0 Mutation rate: 3.5e-09 Recombination rate: 2.782e-09

stdpopsim AedAeg [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, MT, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

AnaPla

Run simulations for Anas platyrhynchos 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 Anas platyrhynchos: Generation time: 4 Population size: 156000 Mutation rate: 4.83e-09 Recombination rate: 1.433e-08

stdpopsim AnaPla [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, 30, chr30, Z, chrZ, 31, chr31, 32, chr32, 33, chr33, 34, chr34, 35, chr35, 36, chr36, 37, chr37, 38, chr38, 39, chr39, 40, chr40

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, Z, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: MallardBlackDuck_2L19

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MallardBlackDuck_2L19. 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

AnoCar

Run simulations for Anolis carolinensis 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 Anolis carolinensis: Generation time: 1.5 Population size: 3050000.0 Mutation rate: 2.1e-10 Recombination rate: 1e-08

stdpopsim AnoCar [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, LGa, LGb, LGc, LGd, LGf, LGg, LGh, MT, chrM

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, LGa, LGb, LGc, LGd, LGf, LGg, LGh, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

AnoGam

Run simulations for Anopheles gambiae 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 Anopheles gambiae: Generation time: 0.09090909090909091 Population size: 1000000.0 Mutation rate: 3.5e-09 Recombination rate: 1.447e-08

stdpopsim AnoGam [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, X, chrX, Mt

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, X, Mt. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: GabonAg1000G_1A17

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: GabonAg1000G_1A17. 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

ApiMel

Run simulations for Apis mellifera 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 Apis mellifera: Generation time: 2 Population size: 200000.0 Mutation rate: 3.4e-09 Recombination rate: 2.318e-07

stdpopsim ApiMel [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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: CM009931.2, NC_037638.1, 1, CM009932.2, NC_037639.1, 2, CM009933.2, NC_037640.1, 3, CM009934.2, NC_037641.1, 4, CM009935.2, NC_037642.1, 5, CM009936.2, NC_037643.1, 6, CM009937.2, NC_037644.1, 7, CM009938.2, NC_037645.1, 8, CM009939.2, NC_037646.1, 9, CM009940.2, NC_037647.1, 10, CM009941.2, NC_037648.1, 11, CM009942.2, NC_037649.1, 12, CM009943.2, NC_037650.1, 13, CM009944.2, NC_037651.1, 14, CM009945.2, NC_037652.1, 15, CM009946.2, NC_037653.1, 16, CM009947.2, NC_001566.1, MT

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: CM009931.2, CM009932.2, CM009933.2, CM009934.2, CM009935.2, CM009936.2, CM009937.2, CM009938.2, CM009939.2, CM009940.2, CM009941.2, CM009942.2, CM009943.2, CM009944.2, CM009945.2, CM009946.2, CM009947.2. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

AraTha

Run simulations for Arabidopsis thaliana 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 Arabidopsis thaliana: Generation time: 1.0 Population size: 10000 Mutation rate: 7e-09 Recombination rate: 8.029e-10

stdpopsim AraTha [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
                 [--help-dfes [HELP_DFES]] [-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]
                 [--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
                 [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: SalomeAveraged_TAIR10

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: SalomeAveraged_TAIR10.

--help-dfes

Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, Mt, Pt

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, Mt, Pt. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18. Please see –help-models for details of these models.

--dfe

Possible choices: Gamma_H18

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_H18. 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.

--help-annotations

Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations

--dfe-annotation

Possible choices: araport_11_exons, araport_11_CDS

Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: araport_11_exons, araport_11_CDS.

-o, --output

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

BosTau

Run simulations for Bos taurus 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 Bos taurus: Generation time: 5 Population size: 62000 Mutation rate: 1.2e-08 Recombination rate: 9.26e-09

stdpopsim BosTau [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, X, chrX, MT, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, X, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: HolsteinFriesian_1M13

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: HolsteinFriesian_1M13. 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

CaeEle

Run simulations for Caenorhabditis elegans 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 Caenorhabditis elegans: Generation time: 0.01 Population size: 10000 Mutation rate: 1.854e-09 Recombination rate: 3.053e-11

stdpopsim CaeEle [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: RockmanRIAIL_ce11

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: RockmanRIAIL_ce11.

-c, --chromosome

Possible choices: I, II, III, IV, V, X, MtDNA

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, X, MtDNA. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

CanFam

Run simulations for Canis familiaris 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 Canis familiaris: Generation time: 3 Population size: 13000 Mutation rate: 4e-09 Recombination rate: 9.506e-09

stdpopsim CanFam [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: Campbell2016_CanFam3_1

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: Campbell2016_CanFam3_1.

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, 30, chr30, 31, chr31, 32, chr32, 33, chr33, 34, chr34, 35, chr35, 36, chr36, 37, chr37, 38, chr38, X, chrX, MT, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, X, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

ChlRei

Run simulations for Chlamydomonas reinhardtii 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 Chlamydomonas reinhardtii: Generation time: 0.001141552511415525 Population size: 1.3999999999999998e-07 Mutation rate: 9.351e-10 Recombination rate: 1.459e-10

stdpopsim ChlRei [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

DroMel

Run simulations for Drosophila melanogaster 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 Drosophila melanogaster: Generation time: 0.1 Population size: 1720600 Mutation rate: 5.49e-09 Recombination rate: 2.085e-08

stdpopsim DroMel [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
                 [--help-dfes [HELP_DFES]] [-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]
                 [--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
                 [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: ComeronCrossover_dm6, ComeronCrossoverV2_dm6

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: ComeronCrossover_dm6, ComeronCrossoverV2_dm6.

--help-dfes

Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs

-c, --chromosome

Possible choices: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, 4, chr4, X, chrX, Y, chrY, mitochondrion_genome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: African3Epoch_1S16, OutOfAfrica_2L06

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: African3Epoch_1S16, OutOfAfrica_2L06. Please see –help-models for details of these models.

--dfe

Possible choices: Gamma_H17, LognormalPlusPositive_R16

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_H17, LognormalPlusPositive_R16. 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.

--help-annotations

Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations

--dfe-annotation

Possible choices: FlyBase_BDGP6.32.51_exons, FlyBase_BDGP6.32.51_CDS

Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: FlyBase_BDGP6.32.51_exons, FlyBase_BDGP6.32.51_CDS.

-o, --output

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

DroSec

Run simulations for Drosophila sechellia 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 Drosophila sechellia: Generation time: 0.05 Population size: 100000 Mutation rate: 1.5e-09 Recombination rate: 2.223e-08

stdpopsim DroSec [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, X, chrX, 4, chr4

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, X, 4. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

EscCol

Run simulations for Escherichia coli 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 Escherichia coli: Generation time: 3.805175e-05 Population size: 180000000.0 Mutation rate: 8.9e-11 Recombination rate: 8.9e-11 Bacterial recombination with tract length: 542

stdpopsim EscCol [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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: Chromosome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: Chromosome. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

GasAcu

Run simulations for Gasterosteus aculeatus 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 Gasterosteus aculeatus: Generation time: 2 Population size: 10000.0 Mutation rate: 3.7e-08 Recombination rate: 3.001e-08

stdpopsim GasAcu [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

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

-b, --bibtex-file

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

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, Y, MT

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, Y, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

HelAnn

Run simulations for Helianthus annuus 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 Helianthus annuus: Generation time: 1.0 Population size: 673968 Mutation rate: 6.1e-09 Recombination rate: 4e-09

stdpopsim HelAnn [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

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

-b, --bibtex-file

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

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

HelMel

Run simulations for Heliconius melpomene 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 Heliconius melpomene: Generation time: 0.0958904109589041 Population size: 2111109 Mutation rate: 2.9e-09 Recombination rate: 3.966e-08

stdpopsim HelMel [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

HomSap

Run simulations for Homo sapiens 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 Homo sapiens: Generation time: 30 Population size: 10000 Mutation rate: 1.29e-08 Recombination rate: 1.253e-08

stdpopsim HomSap [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
                 [--help-dfes [HELP_DFES]] [-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]
                 [--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
                 [-o OUTPUT]
                 samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: HapMapII_GRCh37, HapMapII_GRCh38, DeCodeSexAveraged_GRCh36, DeCodeSexAveraged_GRCh38, PyrhoACB_GRCh38, PyrhoASW_GRCh38, PyrhoBEB_GRCh38, PyrhoCDX_GRCh38, PyrhoCEU_GRCh38, PyrhoCHB_GRCh38, PyrhoCHS_GRCh38, PyrhoCLM_GRCh38, PyrhoESN_GRCh38, PyrhoFIN_GRCh38, PyrhoGBR_GRCh38, PyrhoGIH_GRCh38, PyrhoGWD_GRCh38, PyrhoIBS_GRCh38, PyrhoITU_GRCh38, PyrhoJPT_GRCh38, PyrhoKHV_GRCh38, PyrhoLWK_GRCh38, PyrhoMSL_GRCh38, PyrhoMXL_GRCh38, PyrhoPEL_GRCh38, PyrhoPJL_GRCh38, PyrhoPUR_GRCh38, PyrhoSTU_GRCh38, PyrhoTSI_GRCh38, PyrhoYRI_GRCh38

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: HapMapII_GRCh37, HapMapII_GRCh38, DeCodeSexAveraged_GRCh36, DeCodeSexAveraged_GRCh38, PyrhoACB_GRCh38, PyrhoASW_GRCh38, PyrhoBEB_GRCh38, PyrhoCDX_GRCh38, PyrhoCEU_GRCh38, PyrhoCHB_GRCh38, PyrhoCHS_GRCh38, PyrhoCLM_GRCh38, PyrhoESN_GRCh38, PyrhoFIN_GRCh38, PyrhoGBR_GRCh38, PyrhoGIH_GRCh38, PyrhoGWD_GRCh38, PyrhoIBS_GRCh38, PyrhoITU_GRCh38, PyrhoJPT_GRCh38, PyrhoKHV_GRCh38, PyrhoLWK_GRCh38, PyrhoMSL_GRCh38, PyrhoMXL_GRCh38, PyrhoPEL_GRCh38, PyrhoPJL_GRCh38, PyrhoPUR_GRCh38, PyrhoSTU_GRCh38, PyrhoTSI_GRCh38, PyrhoYRI_GRCh38.

--help-dfes

Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, Y, chrY, MT, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B11, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21. Please see –help-models for details of these models.

--dfe

Possible choices: Gamma_K17, Gamma_H17

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_K17, Gamma_H17. 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.

--help-annotations

Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations

--dfe-annotation

Possible choices: ensembl_havana_104_exons, ensembl_havana_104_CDS

Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: ensembl_havana_104_exons, ensembl_havana_104_CDS.

-o, --output

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

PanTro

Run simulations for Pan troglodytes 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 Pan troglodytes: Generation time: 24.6 Population size: 16781 Mutation rate: 1.6e-08 Recombination rate: 1.2e-08

stdpopsim PanTro [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, chr1, 2A, chr2A, 2B, chr2B, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, Y, chrY

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2A, 2B, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: BonoboGhost_4K19

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BonoboGhost_4K19. 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

PapAnu

Run simulations for Papio anubis 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 Papio anubis: Generation time: 11 Population size: 335505 Mutation rate: 5.7e-09 Recombination rate: 1.124e-08

stdpopsim PapAnu [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: Pyrho_PAnubis1_0

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: Pyrho_PAnubis1_0.

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: SinglePopSMCpp_1W22

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SinglePopSMCpp_1W22. 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

PonAbe

Run simulations for Pongo abelii 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 Pongo abelii: Generation time: 25 Population size: 17900.0 Mutation rate: 1.5e-08 Recombination rate: 6.403e-09

stdpopsim PonAbe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
                 [--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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.

--help-genetic-maps

Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps

-D, --dry-run

Do not run actual simulation

Default: False

-g, --genetic-map

Possible choices: NaterPA_PonAbe3, NaterPP_PonAbe3

Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: NaterPA_PonAbe3, NaterPP_PonAbe3.

-c, --chromosome

Possible choices: 1, chr1, 2A, 2a, chr2a, chr2A, 2B, 2b, chr2b, chr2B, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, MT, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2A, 2B, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, MT. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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: TwoSpecies_2L11

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: TwoSpecies_2L11. 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

StrAga

Run simulations for Streptococcus agalactiae 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 Streptococcus agalactiae: Generation time: 0.0027397260273972603 Population size: 140000 Mutation rate: 1.53e-09 Recombination rate: 1.53e-10 Bacterial recombination with tract length: 120000

stdpopsim StrAga [-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 samples must be specified. The number of arguments that will be accepted depends on the simulation model that is specified: 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, I, chr1

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1. 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

Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

Default: 1

--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

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . 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

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.

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