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Welcome to slim-discuss! Please find general information and downloads for SLiM at http://messerlab.org/slim/. There is a free online SLiM workshop at http://benhaller.com/workshops/workshops.html.

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Kamolphat Atsawawaranunt, … Ben Haller6

May 21

Using msprime to simulate initial populations with multiple chromosome in SLiM 5.0

Hi A! OK, complicated. I don't think there's anything wrong with your model, at least not

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Using msprime to simulate initial populations with multiple chromosome in SLiM 5.0

Hi A! OK, complicated. I don't think there's anything wrong with your model, at least not

May 21

Prothama Manna, Ben Haller2

May 21

Calculate Ne

Hi Prothama! Section 9.11 of the manual has a little discussion of effective population size

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Calculate Ne

Hi Prothama! Section 9.11 of the manual has a little discussion of effective population size

May 21

Peter Ralph, Philip Wolper3

May 20

pyslim 1.1 beta release

The new docs are at https://tskit.dev/pyslim/docs/latest/introduction.html see in particular https://

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pyslim 1.1 beta release

The new docs are at https://tskit.dev/pyslim/docs/latest/introduction.html see in particular https://

May 20

yang lu, … Peter Ralph4

May 13

Extracting ancestral tracts from admixed population in two population admixture model by slim and tskit

No worries, Yang! Best of luck. On Tue, May 13, 2025 at 5:51 AM yang lu <yanglu12...@126.com

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Extracting ancestral tracts from admixed population in two population admixture model by slim and tskit

No worries, Yang! Best of luck. On Tue, May 13, 2025 at 5:51 AM yang lu <yanglu12...@126.com

May 13

Kamolphat Atsawawaranunt, Ben Haller5

May 9

Life-long sexual monogamy

Hi A! You found a bug in the recipe, thanks! The line that reads: tag_counts = tabulate(tags, maxbin=

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Life-long sexual monogamy

Hi A! You found a bug in the recipe, thanks! The line that reads: tag_counts = tabulate(tags, maxbin=

May 9

Jiseon Min, Peter Ralph2

May 9

Genomic element type without mutation + tree sequence recording?

Hi, Jiseon! Well, here's an example of a chromosome with only selected mutations happening in a

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Genomic element type without mutation + tree sequence recording?

Hi, Jiseon! Well, here's an example of a chromosome with only selected mutations happening in a

May 9

Viv, Ben Haller3

May 7

Sex-specific monogamy

Ah its the sampling down bit I was missing. That's been a great help. Thank you! On Wednesday,

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Sex-specific monogamy

Ah its the sampling down bit I was missing. That's been a great help. Thank you! On Wednesday,

May 7

Alfredo Antonio Reis Marin, Ben Haller2

May 3

Best way to track mutation segregation time?

Hi Alfredo! This is a nice problem for illustrating that you *can* retain references to mutations

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Best way to track mutation segregation time?

Hi Alfredo! This is a nice problem for illustrating that you *can* retain references to mutations

May 3

font...@gmail.com, Ben Haller4

May 2

subpopulation/individual info on exported VCF?

Hi JP! Glad to hear the new outputIndividualsToVCF() method is a good fit for you! :-> It's

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subpopulation/individual info on exported VCF?

Hi JP! Glad to hear the new outputIndividualsToVCF() method is a good fit for you! :-> It's

May 2

Ben Haller2

Apr 22

SLiM 5.0 released

Hi folks. The Windows pacman installer is now available for SLiM 5.0. We are still waiting on

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SLiM 5.0 released

Hi folks. The Windows pacman installer is now available for SLiM 5.0. We are still waiting on

Apr 22

siqi liu, Ben Haller5

Apr 15

addRecombinant() function

Hi Ben, Thanks again! I've decided to simplify my simulation — I'll go with performing two

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addRecombinant() function

Hi Ben, Thanks again! I've decided to simplify my simulation — I'll go with performing two

Apr 15

Darren Li, … Ben Haller5

Apr 14

quantile() function

I've used rank() to compute quantiles as Peter suggested, but a bit modified: normalized_ranks

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quantile() function

I've used rank() to compute quantiles as Peter suggested, but a bit modified: normalized_ranks

Apr 14

John Michael Basaca, Peter Ralph2

Apr 14

Using tree sequence file to start a nucleotide-based SLiM simulation

Hi, John - good question. There's just one minor thing to do, and you're almost there, but

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Using tree sequence file to start a nucleotide-based SLiM simulation

Hi, John - good question. There's just one minor thing to do, and you're almost there, but

Apr 14

Philip Wolper, … Ben Haller5

Apr 11

Moran model

Hi Philip! I added it to SLiM-Extras yesterday, actually. :-> It can be found here: https://github

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Moran model

Hi Philip! I added it to SLiM-Extras yesterday, actually. :-> It can be found here: https://github

Apr 11

Dan Schrider, Ben Haller5

Apr 11

Checking gene conversion events in recombination() callback

No that makes perfect sense. Obviously my brain had totally shut down last night... Thanks! Dan On

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Checking gene conversion events in recombination() callback

No that makes perfect sense. Obviously my brain had totally shut down last night... Thanks! Dan On

Apr 11

Alejandra Jimenez, … Curro Campuzano3

Mar 28

Renaming tree sequence output files within a job array

What about this approach? I usually send the tree sequence output to standard output (using the `/dev

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Renaming tree sequence output files within a job array

What about this approach? I usually send the tree sequence output to standard output (using the `/dev

Mar 28

Prothama Manna, Ben Haller2

Mar 27

Weird result of overdominance

Hi Prothama! This is really a population genetics question, not a SLiM question, so it's outside

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Weird result of overdominance

Hi Prothama! This is really a population genetics question, not a SLiM question, so it's outside

Mar 27

Héctor Alessandro López Hérnandez, Ben Haller2

Mar 24

Error in addRecombination

Hi Héctor! That error message is telling you that the function addRecombinant() has another parameter

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Error in addRecombination

Hi Héctor! That error message is telling you that the function addRecombinant() has another parameter

Mar 24

Jules Bonte, Ben Haller2

Mar 24

Rotational migration

I think that is perhaps because of the problems in the reproduction() callback that I mentioned. If

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Rotational migration

I think that is perhaps because of the problems in the reproduction() callback that I mentioned. If

Mar 24

Jules Bonte, Ben Haller2

Mar 24

Rotational migration

Hi Jules! Some observations as I look at your script: - you're setting self.active to 1 at the

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Rotational migration

Hi Jules! Some observations as I look at your script: - you're setting self.active to 1 at the

Mar 24

clarka...@gmail.com, Ben Haller5

Mar 23

Windows installation problem

Ok, we found a solution. It appears that for some reason SLiMgui is opening minimised by default. So,

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Windows installation problem

Ok, we found a solution. It appears that for some reason SLiMgui is opening minimised by default. So,

Mar 23

Bunga Tiasyaira, Ben Haller4

Mar 23

SLiM Mysteriously stops after first generation

Hi Ben! Thanks a lot for the quick reply; I just made my events ran for .trees that began at much

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SLiM Mysteriously stops after first generation

Hi Ben! Thanks a lot for the quick reply; I just made my events ran for .trees that began at much

Mar 23

Noam Vogt-Vincent, Ben Haller3

Mar 21

Automatically logging output for subpopulations individually

Awesome, thank you for the workaround! On Thursday, 20 March 2025 at 17:31:53 UTC-10 Ben Haller wrote

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Automatically logging output for subpopulations individually

Awesome, thank you for the workaround! On Thursday, 20 March 2025 at 17:31:53 UTC-10 Ben Haller wrote

Mar 21

Harald Kundl, Ben Haller4

Mar 20

Re: Incorporation of partheno stages

Hi Harald! As I've said in other replies today, sorry for my lack of attention lately, as I had

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Re: Incorporation of partheno stages

Hi Harald! As I've said in other replies today, sorry for my lack of attention lately, as I had

Mar 20

Noam Vogt-Vincent, Ben Haller6

Mar 20

Efficiently translating a vector with a dictionary

Hi Ben, Thank you for your reply! Sorry, to be clear, that code was just a contrived example to

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Efficiently translating a vector with a dictionary

Hi Ben, Thank you for your reply! Sorry, to be clear, that code was just a contrived example to

Mar 20

Autumn Allemon, … Ben Haller9

Mar 20

Keeping Neutral populations after introgression of a beneficial allele to 1 population after migration

Hi Autumn, Sorry for the slow reply; I've had friends visiting and other complications. (And see

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Keeping Neutral populations after introgression of a beneficial allele to 1 population after migration

Hi Autumn, Sorry for the slow reply; I've had friends visiting and other complications. (And see

Mar 20

Yash Kulkarni, Ben Haller3

Mar 20

Setting up a neutral simulation from a VCF output

Hello Ben, Thanks a lot for the reply! Will see what I can do. Best regards, Yash On Fri, 21 Mar,

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Setting up a neutral simulation from a VCF output

Hello Ben, Thanks a lot for the reply! Will see what I can do. Best regards, Yash On Fri, 21 Mar,

Mar 20

Christopher McAllester, … Ben Haller6

Mar 14

Hi folks! Sorry I've been offline for a while in this discussion! Friends visiting from out of

unread,

Hi folks! Sorry I've been offline for a while in this discussion! Friends visiting from out of

Mar 14

Rose Huang, … Curro Campuzano4

Mar 14

Questions on treeseq and application on genome with different genomic element types

Thank you so much Ben, this is very helpful and exactly what I need! Best, Rose On Wednesday, March

unread,

Questions on treeseq and application on genome with different genomic element types

Thank you so much Ben, this is very helpful and exactly what I need! Best, Rose On Wednesday, March

Mar 14

C Henry, Ben Haller2

Mar 13

Question about heterozygosity calculations

Hi C! I'm not sure what might be causing this. It looks like it might be a bug, but I'm not

unread,

Question about heterozygosity calculations

Hi C! I'm not sure what might be causing this. It looks like it might be a bug, but I'm not

Mar 13