slim-discuss

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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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Darren Li

Aug 28

Efficiently reading from a dictionary

Hello everyone, I have a dataframe/dictionary of values from which I want to get a specific value (

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Efficiently reading from a dictionary

Hello everyone, I have a dataframe/dictionary of values from which I want to get a specific value (

Aug 28

Hannes Becher, … Ben Haller5

Aug 28

Per-gene properties that affect selection coefficients

Hi Hannes and Peter, Perhaps a useful addendum to this discussion is that: (1) the GenomicElement

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Per-gene properties that affect selection coefficients

Hi Hannes and Peter, Perhaps a useful addendum to this discussion is that: (1) the GenomicElement

Aug 28

Ellie Weise, Ben Haller2

Aug 28

Adjusting VCF Sample Output

Hi Ellie! The outputIndividuals() and outputIndividualsToVCF() methods can be called on any vector of

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Adjusting VCF Sample Output

Hi Ellie! The outputIndividuals() and outputIndividualsToVCF() methods can be called on any vector of

Aug 28

Michael Kopp, Ben Haller2

Aug 26

Graph mutation frequency trajectories not working

Hi Michael! The plot (probably) works correctly, but it has a quirk that needs to be better handled

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Graph mutation frequency trajectories not working

Hi Michael! The plot (probably) works correctly, but it has a quirk that needs to be better handled

Aug 26

Peter Ralph

Aug 18

pyslim 1.1.0 released

Hello, all - I've just released version 1.1.0 of pyslim, which is provided to go along with SLiM

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pyslim 1.1.0 released

Hello, all - I've just released version 1.1.0 of pyslim, which is provided to go along with SLiM

Aug 18

Sohan Alleshwaram, … Ben Haller5

Aug 12

Using a Burn-in to Interpolate Nucleotide Sequences Across Space

Hi Sohan, Ah, I see. I was misled by the term "burn-in", which normally does involve new

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Using a Burn-in to Interpolate Nucleotide Sequences Across Space

Hi Sohan, Ah, I see. I was misled by the term "burn-in", which normally does involve new

Aug 12

John Michael Basaca, Peter Ralph2

Aug 12

error in reading pyslim burnin trees file in SLiM 5.0

IIUC, you've generated a tree sequence entirely in python (eg, by doing msprime + pyslim.annotate

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error in reading pyslim burnin trees file in SLiM 5.0

IIUC, you've generated a tree sequence entirely in python (eg, by doing msprime + pyslim.annotate

Aug 12

Ben Haller

Aug 12

SLiM 5 paper is posted in bioRxiv

Hi all! Just a quick note that the SLiM 5 paper is now up on bioRxiv: https://doi.org/10.1101/2025.08

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SLiM 5 paper is posted in bioRxiv

Hi all! Just a quick note that the SLiM 5 paper is now up on bioRxiv: https://doi.org/10.1101/2025.08

Aug 12

Grace Rhodes, Ben Haller2

Aug 7

fitnessEffect() callback for loss-of-function recessive effect

Hi Grace! I'm traveling right now so I'm not in a position to look into this much at the

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fitnessEffect() callback for loss-of-function recessive effect

Hi Grace! I'm traveling right now so I'm not in a position to look into this much at the

Aug 7

Boki Lai, … Jose Luis Mijangos6

Aug 5

Simulated FST value ~1/4 of the expected theoretical value

Thank you for the information and advice! It's very helpful. Blessings, Ariel Jose Luis Mijangos

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Simulated FST value ~1/4 of the expected theoretical value

Thank you for the information and advice! It's very helpful. Blessings, Ariel Jose Luis Mijangos

Aug 5

John Michael Basaca, Peter Ralph7

Jul 31

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

Thank you for your guidance, Peter! You're right! I was able to successfully produce a VCF file

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

Thank you for your guidance, Peter! You're right! I was able to successfully produce a VCF file

Jul 31

Dan Kehila, Ben Haller2

Jul 18

Neutral modifiers in SLiM

Hi Dan! I did a google scholar search on ""slim" modifier mutation affecting

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Neutral modifiers in SLiM

Hi Dan! I did a google scholar search on ""slim" modifier mutation affecting

Jul 18

Luis, Ben Haller4

Jul 11

Segmentation fault in Linux server

Hi Luis! Let's take this off-list. It does sound like it is probably a SLiM bug of some kind,

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Segmentation fault in Linux server

Hi Luis! Let's take this off-list. It does sound like it is probably a SLiM bug of some kind,

Jul 11

Jack Sissons, … Ben Haller3

Jul 7

Looking for anyone in New Zealand or Australia who wants to learn SLiM

Hi A and others, Please follow up with Jack and Ali off-list. Postings here go to several hundred

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Looking for anyone in New Zealand or Australia who wants to learn SLiM

Hi A and others, Please follow up with Jack and Ali off-list. Postings here go to several hundred

Jul 7

Ben Haller

Jun 17

SLiM Workshop online materials updated for SLiM 5.0

Hi folks! Just a quick announcement that the SLiM Workshop's online materials have been updated

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SLiM Workshop online materials updated for SLiM 5.0

Hi folks! Just a quick announcement that the SLiM Workshop's online materials have been updated

Jun 17

Kamolphat Atsawawaranunt, … Ben Haller12

Jun 16

calcFST() in SLiM 5.0 multichromosome model

Hi A, Yes, as you say there are many different ways to calculate FST, and other pop-gen statistics as

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calcFST() in SLiM 5.0 multichromosome model

Hi A, Yes, as you say there are many different ways to calculate FST, and other pop-gen statistics as

Jun 16

Rodolfo, … Martin Petr5

Jun 10

Using a demes-format file in SLiM to simulate under a realistic demographic model

Hi all, Thanks for the ping, Ben. I'm afraid slendr won't be of much help in this instance. I

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Using a demes-format file in SLiM to simulate under a realistic demographic model

Hi all, Thanks for the ping, Ben. I'm afraid slendr won't be of much help in this instance. I

Jun 10

Ben Haller

Jun 9

Looking for a SLiM Workshop guest speaker

Hi folks! I'm posting with an unusual request. I generally like to have two guest lectures on the

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Looking for a SLiM Workshop guest speaker

Hi folks! I'm posting with an unusual request. I generally like to have two guest lectures on the

Jun 9

Prothama Manna, Ben Haller2

Jun 3

Duplicate Mutations at the Same Chromosomal Position in VCF Outputs

Hi Prothama, You can certainly have mutation A arise in one individual at position P, and mutation B

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Duplicate Mutations at the Same Chromosomal Position in VCF Outputs

Hi Prothama, You can certainly have mutation A arise in one individual at position P, and mutation B

Jun 3

Vítor Sudbrack, Ben Haller2

May 28

calcDxy() function

Hi Vitor! Hmm, I wrote a reply to this, and Google Groups seems to have eaten it, so I'll write

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calcDxy() function

Hi Vitor! Hmm, I wrote a reply to this, and Google Groups seems to have eaten it, so I'll write

May 28

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