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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/worksh
ops/workshops.html
.
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Kamolphat Atsawawaranunt
, …
Ben Haller
6
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
unread,
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 Haller
2
May 21
Calculate Ne
Hi Prothama! Section 9.11 of the manual has a little discussion of effective population size
unread,
Calculate Ne
Hi Prothama! Section 9.11 of the manual has a little discussion of effective population size
May 21
Peter Ralph
,
Philip Wolper
3
May 20
pyslim 1.1 beta release
The new docs are at https://tskit.dev/pyslim/docs/latest/introduction.html see in particular https://
unread,
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 Ralph
4
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
unread,
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 Haller
5
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=
unread,
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 Ralph
2
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
unread,
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 Haller
3
May 7
Sex-specific monogamy
Ah its the sampling down bit I was missing. That's been a great help. Thank you! On Wednesday,
unread,
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 Haller
2
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
unread,
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 Haller
4
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
unread,
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 Haller
2
Apr 22
SLiM 5.0 released
Hi folks. The Windows pacman installer is now available for SLiM 5.0. We are still waiting on
unread,
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 Haller
5
Apr 15
addRecombinant() function
Hi Ben, Thanks again! I've decided to simplify my simulation — I'll go with performing two
unread,
addRecombinant() function
Hi Ben, Thanks again! I've decided to simplify my simulation — I'll go with performing two
Apr 15
Darren Li
, …
Ben Haller
5
Apr 14
quantile() function
I've used rank() to compute quantiles as Peter suggested, but a bit modified: normalized_ranks
unread,
quantile() function
I've used rank() to compute quantiles as Peter suggested, but a bit modified: normalized_ranks
Apr 14
John Michael Basaca
,
Peter Ralph
2
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
unread,
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 Haller
5
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 Haller
5
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
unread,
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 Campuzano
3
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
unread,
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 Haller
2
Mar 27
Weird result of overdominance
Hi Prothama! This is really a population genetics question, not a SLiM question, so it's outside
unread,
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 Haller
2
Mar 24
Error in addRecombination
Hi Héctor! That error message is telling you that the function addRecombinant() has another parameter
unread,
Error in addRecombination
Hi Héctor! That error message is telling you that the function addRecombinant() has another parameter
Mar 24
Jules Bonte
,
Ben Haller
2
Mar 24
Rotational migration
I think that is perhaps because of the problems in the reproduction() callback that I mentioned. If
unread,
Rotational migration
I think that is perhaps because of the problems in the reproduction() callback that I mentioned. If
Mar 24
Jules Bonte
,
Ben Haller
2
Mar 24
Rotational migration
Hi Jules! Some observations as I look at your script: - you're setting self.active to 1 at the
unread,
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 Haller
5
Mar 23
Windows installation problem
Ok, we found a solution. It appears that for some reason SLiMgui is opening minimised by default. So,
unread,
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 Haller
4
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
unread,
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 Haller
3
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
unread,
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 Haller
4
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
unread,
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 Haller
6
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
unread,
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 Haller
9
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
unread,
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 Haller
3
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,
unread,
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 Haller
6
Mar 14
VS Code & related editor syntax highlighting extension for slim/eidos
Hi folks! Sorry I've been offline for a while in this discussion! Friends visiting from out of
unread,
VS Code & related editor syntax highlighting extension for slim/eidos
Hi folks! Sorry I've been offline for a while in this discussion! Friends visiting from out of
Mar 14
Rose Huang
, …
Curro Campuzano
4
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 Haller
2
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