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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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Manas G. A.
, …
Peter Ralph
5
Jul 26
Changing selection coefficients and loading from a .trees file
Hi Ben! Thanks for your response. What I would really like to do is the following: Step (1) - Run a
unread,
Changing selection coefficients and loading from a .trees file
Hi Ben! Thanks for your response. What I would really like to do is the following: Step (1) - Run a
Jul 26
Stylianos Mavrianos
,
Ben Haller
3
Jul 26
Help with Simulating Beneficial SNP and Linked Neutral Mutations
Hi Ben, Thank you very much for your quick answer, I will look into it. Best, Stylianos On Thursday,
unread,
Help with Simulating Beneficial SNP and Linked Neutral Mutations
Hi Ben, Thank you very much for your quick answer, I will look into it. Best, Stylianos On Thursday,
Jul 26
STEVEN VAN BELLEGHEM
,
Ben Haller
2
Jul 25
empty population and chromosome view window
Hmm. Well, those two views are drawn using OpenGL, whereas all the other views in the window are not.
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empty population and chromosome view window
Hmm. Well, those two views are drawn using OpenGL, whereas all the other views in the window are not.
Jul 25
Augustin Desprez
,
Ben Haller
5
Jul 24
General : is SLiM able to simulate plant breeding ?
Thank you very much for your answer, I will look into it. I may do a feedback in a few weeks/months
unread,
General : is SLiM able to simulate plant breeding ?
Thank you very much for your answer, I will look into it. I may do a feedback in a few weeks/months
Jul 24
João Pedro Meireles
, …
Ben Haller
6
Jul 16
Giving name to populations
Hey all. Just following up on this thread about user-assigned names for subpopulations. I've just
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Giving name to populations
Hey all. Just following up on this thread about user-assigned names for subpopulations. I've just
Jul 16
Ben Haller
Jul 15
SLiM at the Evolution conference in Montreal
Hi folks! Just a quick post to let you all know that I will be at the Evolution conference in
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SLiM at the Evolution conference in Montreal
Hi folks! Just a quick post to let you all know that I will be at the Evolution conference in
Jul 15
Viv
,
Ben Haller
6
Jul 14
Sampling siblings
Hi Viv! I tweaked your output code a bit to help investigate this: ids = p1.individuals.
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Sampling siblings
Hi Viv! I tweaked your output code a bit to help investigate this: ids = p1.individuals.
Jul 14
Ekaterina Korotkevich
,
Ben Haller
2
Jul 12
Modeling back mutations for haploid organisms
Hi Ekaterina! I'd recommend you look at section 18.15; it is geared towards nucleotide-based
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Modeling back mutations for haploid organisms
Hi Ekaterina! I'd recommend you look at section 18.15; it is geared towards nucleotide-based
Jul 12
Eugenio López Cortegano
, …
Ben Haller
5
Jul 9
What is the Eidos equivalent of the R operator %in% ?
Yes, Peter's solution is better as long as the tag values are unique – in other words, as long as
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What is the Eidos equivalent of the R operator %in% ?
Yes, Peter's solution is better as long as the tag values are unique – in other words, as long as
Jul 9
Peter Ralph
Jul 5
syntax highlighting of SLiM code in LaTeX
Hi, all - some of you might find the following useful. Here: https://github.com/MesserLab/SLiM-Extras
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syntax highlighting of SLiM code in LaTeX
Hi, all - some of you might find the following useful. Here: https://github.com/MesserLab/SLiM-Extras
Jul 5
João Pedro Meireles
, …
Peter Ralph
5
Jul 5
Simulating a reintroduction programme (ex situ to in situ)
Hello Victor Quick question: I just came from reading your publication (Amazing btw). In your
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Simulating a reintroduction programme (ex situ to in situ)
Hello Victor Quick question: I just came from reading your publication (Amazing btw). In your
Jul 5
Yazzi McDonough
,
Ben Haller
2
Jul 4
Simulating autosomes and X-chromosomes (at the same time)
Hi Yazzi! Your approach sounds good, and you found the relevant sections – 14.5, in particular. Note
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Simulating autosomes and X-chromosomes (at the same time)
Hi Yazzi! Your approach sounds good, and you found the relevant sections – 14.5, in particular. Note
Jul 4
Débora Brandt
, …
Miguel de Navascués
7
Jun 28
output tree sequence for subset of individuals
Thanks, that is very helpful! I might try to use that trick. I just wanted to add a note that I
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output tree sequence for subset of individuals
Thanks, that is very helpful! I might try to use that trick. I just wanted to add a note that I
Jun 28
Peter Laurin
, …
Peter Ralph
6
Jun 27
Not achieving expected diversity metrics in simple diploid and haploid simulations
Thanks I'll try this out! Peter On Thursday, June 27, 2024 at 10:15:05 AM UTC-7 Peter Ralph wrote
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Not achieving expected diversity metrics in simple diploid and haploid simulations
Thanks I'll try this out! Peter On Thursday, June 27, 2024 at 10:15:05 AM UTC-7 Peter Ralph wrote
Jun 27
Grace Rhodes
, …
Peter Ralph
3
Jun 16
Adapting Gravel et al Recipe to Include Increased Growth Rate In Recent Epoch
I agree with Chase (thanks!). But, let me add one more thing - "what's expected" from
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Adapting Gravel et al Recipe to Include Increased Growth Rate In Recent Epoch
I agree with Chase (thanks!). But, let me add one more thing - "what's expected" from
Jun 16
Ravi Vishwakarma
,
Ben Haller
5
Jun 13
Sampling individuals and calculating microsat expected Heterozygosity
So, Ravi is having trouble posting to the group (if you have difficulties, I recommend using the web
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Sampling individuals and calculating microsat expected Heterozygosity
So, Ravi is having trouble posting to the group (if you have difficulties, I recommend using the web
Jun 13
Padovani, Giada
,
Ben Haller
5
Jun 13
same SpatialMap for two subpopulations
No worries, this feature is a bit hidden – probably somebody else just learned about it because of
unread,
same SpatialMap for two subpopulations
No worries, this feature is a bit hidden – probably somebody else just learned about it because of
Jun 13
Jared Grummer
,
Ben Haller
3
Jun 12
Modeling reproductive skew
Thanks, Ben! I started reading last week and then got sidetracked with some other work. I'll look
unread,
Modeling reproductive skew
Thanks, Ben! I started reading last week and then got sidetracked with some other work. I'll look
Jun 12
Luca Soldini
, …
Peter Ralph
4
Jun 11
Spatial non-WF model - avoiding center
Hi, Luca - the reason seems to be that the spatial position of offspring is not being set explicitly.
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Spatial non-WF model - avoiding center
Hi, Luca - the reason seems to be that the spatial position of offspring is not being set explicitly.
Jun 11
Carlos Sarabia
,
Ben Haller
2
Jun 10
Setting different selection coefficients of the same mutation in different populations
Hi Carlos! Yes, this sort of thing is what a mutationEffect() callback is for (see section 10.2 of
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Setting different selection coefficients of the same mutation in different populations
Hi Carlos! Yes, this sort of thing is what a mutationEffect() callback is for (see section 10.2 of
Jun 10
Mark Hibbins
, …
Ben Haller
3
Jun 7
Mutations with sex-specific DFEs
Thanks Peter! That said, it would be trivial to add an rlaplace() function; I just wait for people to
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Mutations with sex-specific DFEs
Thanks Peter! That said, it would be trivial to add an rlaplace() function; I just wait for people to
Jun 7
Dylan Clark
,
Ben Haller
2
Jun 4
Accidentally sampling genomes from killed individuals
Hi Dylan! No, this is not a concern with your code as designed. As the doc for killIndividuals() says
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Accidentally sampling genomes from killed individuals
Hi Dylan! No, this is not a concern with your code as designed. As the doc for killIndividuals() says
Jun 4
Anushka Jain
,
Ben Haller
2
Jun 3
Simulating HIV sequences
Hi Anushka! So I guess there are two questions here? One is about running MEGAX on your generated
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Simulating HIV sequences
Hi Anushka! So I guess there are two questions here? One is about running MEGAX on your generated
Jun 3
Carlos Sarabia
,
Peter Ralph
2
May 28
SLiMv4.2.2 crashing in Linux, not able to open files externally
Hello, Carlos - I've just built 4.2.2 on my linux machine and not encountered any of these issues
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SLiMv4.2.2 crashing in Linux, not able to open files externally
Hello, Carlos - I've just built 4.2.2 on my linux machine and not encountered any of these issues
May 28
Héctor Alessandro López Hérnandez
,
Ben Haller
2
May 21
Tracking allele frequency of m2 in each subpopulation
Hi Héctor! Thanks for the complete code for this question; that makes it much easier to reproduce the
unread,
Tracking allele frequency of m2 in each subpopulation
Hi Héctor! Thanks for the complete code for this question; that makes it much easier to reproduce the
May 21
Héctor Alessandro López Hérnandez
,
Ben Haller
4
May 21
Having problems with a stepping stone model and get printed frequencies
Hi Héctor, Sorry for the slow reply; life is a bit busy right now. Finished teaching a SLiM workshop
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Having problems with a stepping stone model and get printed frequencies
Hi Héctor, Sorry for the slow reply; life is a bit busy right now. Finished teaching a SLiM workshop
May 21
Ben Haller
2
May 10
SLiM 4.2.2 released
Hi folks. Just a quick followup to say: all SLiM installers are now updated to 4.2.2. That includes
unread,
SLiM 4.2.2 released
Hi folks. Just a quick followup to say: all SLiM installers are now updated to 4.2.2. That includes
May 10
font...@gmail.com
,
Ben Haller
5
May 10
logging results of a user defined function that uses a subset of the population as input
Hi João, Here is a minimal example of using addSuppliedColumn() with automatic logging, by setting
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logging results of a user defined function that uses a subset of the population as input
Hi João, Here is a minimal example of using addSuppliedColumn() with automatic logging, by setting
May 10
Ben Haller
May 9
interview on Data Skeptic podcast
Hey campers. I got interviewed about SLiM for a podcast called Data Skeptic: https://dataskeptic.com/
unread,
interview on Data Skeptic podcast
Hey campers. I got interviewed about SLiM for a podcast called Data Skeptic: https://dataskeptic.com/
May 9
Baron Koylass
,
Peter Ralph
5
Apr 30
Setting a starting allele frequency bias
Hi Peter Ralph, Great! I have actually done a combination of both ways you had proposed. I have now
unread,
Setting a starting allele frequency bias
Hi Peter Ralph, Great! I have actually done a combination of both ways you had proposed. I have now
Apr 30