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Welcome to the msprime-users mailing list! This list is intended as a place where people can ask questions about msprime and share their thoughts on useful potential features. Hopefully, by asking lots of questions we can build an archive of knowledge that future users can find easily via search engines.

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Feb 18

Trouble generating expected PSMC output from constant population model

Hello, Before testing an empirical model in PSMC, we are trying to simulate a simple demographic

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Trouble generating expected PSMC output from constant population model

Hello, Before testing an empirical model in PSMC, we are trying to simulate a simple demographic

Feb 18

Feb 10

Population growth up to present (gen. 0)

Hi Peter, Thanks a lot for the response! I have calculated the growth rate to get the population size

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Population growth up to present (gen. 0)

Hi Peter, Thanks a lot for the response! I have calculated the growth rate to get the population size

Feb 10

7/17/24

integer IDs of populations within the parent Demography

Hi, this may seem like a very simple question, but I wanted to be sure what I suspected to be the

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integer IDs of populations within the parent Demography

Hi, this may seem like a very simple question, but I wanted to be sure what I suspected to be the

7/17/24

2/1/24

Modifying stdpopsim.models.DemographicModel

Hi msprime devs, I'm working with a stdpopsim.models.DemographicModel and was trying to modify

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Modifying stdpopsim.models.DemographicModel

Hi msprime devs, I'm working with a stdpopsim.models.DemographicModel and was trying to modify

2/1/24

3/20/23

how to link each introgressed tract to the indivdiual

Hi everyone, I am running simulations with Msprime to test different chromosome painting methods. I

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how to link each introgressed tract to the indivdiual

Hi everyone, I am running simulations with Msprime to test different chromosome painting methods. I

3/20/23

Richard Kerr, Peter Ralph4

9/28/22

Basic question on recombination_rate and multiple chromosomes in msprime 1.0

Hm, which part do you want more explanation on? The "Poisson model" part or why 2^{-t} is

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Basic question on recombination_rate and multiple chromosomes in msprime 1.0

Hm, which part do you want more explanation on? The "Poisson model" part or why 2^{-t} is

9/28/22

Keric Lamb, LaKisha David2

3/9/22

Basic question regarding msprime VCF writing

I had the same question. I wrote a script to create a pandas dataframe to address this question. I

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Basic question regarding msprime VCF writing

I had the same question. I wrote a script to create a pandas dataframe to address this question. I

3/9/22

Alice Pearson, Peter Ralph3

10/22/21

Yes no problem! On Friday, 22 October 2021 at 00:23:55 UTC+1 Peter Ralph wrote: Hi, Alice - this is a

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Yes no problem! On Friday, 22 October 2021 at 00:23:55 UTC+1 Peter Ralph wrote: Hi, Alice - this is a

10/22/21

pramesh shakya, Peter Ralph4

10/4/21

Tracking IBD boundaries with and without full ARG

Hi Peter, So I just noticed that I was using the un-simplified tree sequence to output the picture of

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Tracking IBD boundaries with and without full ARG

Hi Peter, So I just noticed that I was using the un-simplified tree sequence to output the picture of

10/4/21

zach.h...@tamu.edu, Peter Ralph2

8/31/21

Max diversity (instead of mean) for evaluating IBD in spatial simulations

Hi, Zach - good question! We don't have an easy way to do this specific thing, although it's

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Max diversity (instead of mean) for evaluating IBD in spatial simulations

Hi, Zach - good question! We don't have an easy way to do this specific thing, although it's

8/31/21

JMR JMR, Jerome Kelleher4

5/11/21

Obtaining ancestral/derived state in VCF output

Happy to help! ps. this mailing list is being retired in favour of our discussion boards, https://

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Obtaining ancestral/derived state in VCF output

Happy to help! ps. this mailing list is being retired in favour of our discussion boards, https://

5/11/21

Julien Y. Dutheil, … Julien Dutheil3

5/6/21

Converting the MutationModel in a TreeSequence

Dear Jerome, Thanks a lot! I will switch to GitHub then! Cheers, Julien. Le jeudi 6 mai 2021 à 19:47:

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Converting the MutationModel in a TreeSequence

Dear Jerome, Thanks a lot! I will switch to GitHub then! Cheers, Julien. Le jeudi 6 mai 2021 à 19:47:

5/6/21

Arslan Zaidi, Peter Ralph3

2/23/21

Calling ROH using msprime + pyslim

Ok good to know. Let me try explicitly calling the nodes based on individual IDs and also try

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Calling ROH using msprime + pyslim

Ok good to know. Let me try explicitly calling the nodes based on individual IDs and also try

2/23/21

Armando Arredondo, Jerome Kelleher2

2/5/21

Obtaining the object representation of a command-line simulation

Hi Armando, This isn't accessible, I'm afraid, as the details of parsing the ms command line

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Obtaining the object representation of a command-line simulation

Hi Armando, This isn't accessible, I'm afraid, as the details of parsing the ms command line

2/5/21

Soul Young, Jerome Kelleher3

1/18/21

R2 Decay Across Distance

Ok will do! Thanks On Thursday, January 14, 2021 at 4:55:53 AM UTC-8 Jerome Kelleher wrote: Hi Soul,

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R2 Decay Across Distance

Ok will do! Thanks On Thursday, January 14, 2021 at 4:55:53 AM UTC-8 Jerome Kelleher wrote: Hi Soul,

1/18/21

Raman Lawal, Jerome Kelleher6

12/2/20

zlib_compression

Hi all, Just a quick note that this has now been resolved by a bugfix release of tskit. You can

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zlib_compression

Hi all, Just a quick note that this has now been resolved by a bugfix release of tskit. You can

12/2/20

Rémi Tournebize, Jerome Kelleher2

11/9/20

msprime demography to ms command converter

Hi Rémi, I haven't used it personally, but I think this R package has some facilities for what

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msprime demography to ms command converter

Hi Rémi, I haven't used it personally, but I think this R package has some facilities for what

11/9/20

Richard Kerr, … Peter Ralph7

10/12/20

Understanding Fst

Hi Peter, I am still very much a msprime novice and your suggestion to compute mean individual

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Understanding Fst

Hi Peter, I am still very much a msprime novice and your suggestion to compute mean individual

10/12/20

Miguel Navascués, Peter Ralph2

10/1/20

wrong sequence length after keep_interval()

Hi, Miguel - it's true, what you expect would also make sense, and this is something we debated

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wrong sequence length after keep_interval()

Hi, Miguel - it's true, what you expect would also make sense, and this is something we debated

10/1/20

Richard Kerr, Jerome Kelleher2

9/2/20

Exporting a subset of variants

Hi Richard, The best way is to subset the sites like you've been doing in your other email, and

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Exporting a subset of variants

Hi Richard, The best way is to subset the sites like you've been doing in your other email, and

9/2/20

Richard Kerr, Jerome Kelleher2

9/2/20

load_tables function has been replaced by TableCollection.tree_sequence.

Hi Richard, Welcome to the msprime/tskit community! I looks like the documentation that you're

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load_tables function has been replaced by TableCollection.tree_sequence.

Hi Richard, Welcome to the msprime/tskit community! I looks like the documentation that you're

9/2/20

Jana Obsteter, Jerome Kelleher5

7/7/20

Expected time for tree chromosomes simulation

Great, thanks again, this is really good and helpful information! Cheers, Jana On Tue, 7 Jul 2020 at

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Expected time for tree chromosomes simulation

Great, thanks again, this is really good and helpful information! Cheers, Jana On Tue, 7 Jul 2020 at

7/7/20

Zachary Hancock, … Jerome Kelleher3

6/15/20

invariant sites in FASTA format

No, we haven't done anything around this yet. With msprime 1.0 we'll optionally have discrete

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invariant sites in FASTA format

No, we haven't done anything around this yet. With msprime 1.0 we'll optionally have discrete

6/15/20

Jerome Kelleher

6/9/20

Re: [msprime-users] sampling same population from different time

Hi, This looks fine to me. There's definitely no problem with having samples at different times

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Re: [msprime-users] sampling same population from different time

Hi, This looks fine to me. There's definitely no problem with having samples at different times

6/9/20

qlan...@gmail.com, Peter Ralph2

4/27/20

Recapitulation and recombination maps

Ah ha. I can sort this out. Would you mind opening an issue on pyslim's GitHub page? Ideally with

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Recapitulation and recombination maps

Ah ha. I can sort this out. Would you mind opening an issue on pyslim's GitHub page? Ideally with

4/27/20

Elizabeth Barthelemy, Peter Ralph3

4/3/20

Using population parameter change

Thank you very much! This is very helpful, I hadn't noticed you could supply the demography

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Using population parameter change

Thank you very much! This is very helpful, I hadn't noticed you could supply the demography

4/3/20

Zachary Hancock, Peter Ralph2

4/1/20

BranchLengthStatCalculator

On Wed, Apr 1, 2020 at 5:44 PM Peter Ralph <petre...@gmail.com> wrote: > That API was

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BranchLengthStatCalculator

On Wed, Apr 1, 2020 at 5:44 PM Peter Ralph <petre...@gmail.com> wrote: > That API was

4/1/20

3/28/20

Re: [msprime-users] how are samples combined to form individuals of given ploidy in write_vcf() method?

If ploidy=2, then samples 0 and 1 are combined to make the first one; 2 and 3 to make the second one,

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Re: [msprime-users] how are samples combined to form individuals of given ploidy in write_vcf() method?

If ploidy=2, then samples 0 and 1 are combined to make the first one; 2 and 3 to make the second one,

3/28/20

3/27/20

Extracting IBD segments from .ts files

Hi, in a recent publication from msprime (link here),, exact IBD segments are extracted from msprime

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Extracting IBD segments from .ts files

Hi, in a recent publication from msprime (link here),, exact IBD segments are extracted from msprime

3/27/20

megan...@gmail.com, … Peter Ralph4

3/18/20

Simulations with specified number of segregating sites

Thanks, Jerome! That's helpful. Peter, I want to simulate linked SNPs in this case; I just want

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Simulations with specified number of segregating sites

Thanks, Jerome! That's helpful. Peter, I want to simulate linked SNPs in this case; I just want

3/18/20

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