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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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Kadee Lawrence
, …
Peter Ralph
3
Jun 29
Errors with pyslim.recapitate( )
Hi, Kadee! Let's see: there's some kind of mismatch between where the lineages are in the
unread,
Errors with pyslim.recapitate( )
Hi, Kadee! Let's see: there's some kind of mismatch between where the lineages are in the
Jun 29
Max Shpak
,
Ben Haller
2
Jun 23
introducing multiple copies of a mutation and tracking their frequency
Hi Max. Yes, each call to addNewDrawnMutation() will give you a separate mutational lineage with a
unread,
introducing multiple copies of a mutation and tracking their frequency
Hi Max. Yes, each call to addNewDrawnMutation() will give you a separate mutational lineage with a
Jun 23
Max Shpak
,
Ben Haller
2
Jun 23
questions on conditioning selective sweep on fixation (or establishment)
Hi Max! Regarding your first question: The difference is between mutations still being simulated (
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questions on conditioning selective sweep on fixation (or establishment)
Hi Max! Regarding your first question: The difference is between mutations still being simulated (
Jun 23
MARCEL LUCAS SÁNCHEZ
,
Ben Haller
4
Jun 21
How can I lower the computational demand of my SLiM analysis?
Hi Marcel, To your questions, 1. I think I would suggest that you simulate a chromosome that is
unread,
How can I lower the computational demand of my SLiM analysis?
Hi Marcel, To your questions, 1. I think I would suggest that you simulate a chromosome that is
Jun 21
Mayra Banuelos
,
Ben Haller
6
Jun 16
Modeling a single microsatellite surrounded by 100kb bases
Found the bugs! Just in case it is helpful for anyone in the future, the first thing was to set the
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Modeling a single microsatellite surrounded by 100kb bases
Found the bugs! Just in case it is helpful for anyone in the future, the first thing was to set the
Jun 16
DAVID VENDRAMI
, …
Ben Haller
8
Jun 15
non neutral burn-in for large simulation
Hi Benjamin, Dang, that's true! What a silly oversight. Thank you very much for spotting this!
unread,
non neutral burn-in for large simulation
Hi Benjamin, Dang, that's true! What a silly oversight. Thank you very much for spotting this!
Jun 15
Ben Haller
Jun 14
Re: strange results from allele_frequencies that depend on call to addNewMutation
Hi Jeff. I think the issue must be with your Python script, in some way; everything seems to be
unread,
Re: strange results from allele_frequencies that depend on call to addNewMutation
Hi Jeff. I think the issue must be with your Python script, in some way; everything seems to be
Jun 14
Zuxi Cui
,
Peter Ralph
4
Jun 13
Output format of nucleatide simulation
Well, Chapter 17 of the SLiM manual talks about tree sequence recording in SLiM; then you might look
unread,
Output format of nucleatide simulation
Well, Chapter 17 of the SLiM manual talks about tree sequence recording in SLiM; then you might look
Jun 13
Max Shpak
,
Peter Ralph
2
Jun 9
interfacing SLiM with ms or mspms (rather than msprime) output
Hi, Max! Let's see - it depends what exactly you mean here: - You could probably use this method
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interfacing SLiM with ms or mspms (rather than msprime) output
Hi, Max! Let's see - it depends what exactly you mean here: - You could probably use this method
Jun 9
Max Shpak
,
Ben Haller
2
Jun 6
union of segregating sites across subpopulations
Hi Max, Yes, this sort of thing is exactly the purpose of the output methods on Genome, which are
unread,
union of segregating sites across subpopulations
Hi Max, Yes, this sort of thing is exactly the purpose of the output methods on Genome, which are
Jun 6
Kadee Lawrence
Jun 6
Question on Saving the Output of p1.outputSample(10)
To whom it may concern, I am new to SLiM and attempting to save the sample output rather than the
unread,
Question on Saving the Output of p1.outputSample(10)
To whom it may concern, I am new to SLiM and attempting to save the sample output rather than the
Jun 6
Ben Haller
,
Peter Ralph
2
Jun 5
SLiM 4.0 beta 1 released; PEQG/KITP
Going along with this pre-release is a beta pre-release of pyslim: https://pypi.org/project/pyslim/
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SLiM 4.0 beta 1 released; PEQG/KITP
Going along with this pre-release is a beta pre-release of pyslim: https://pypi.org/project/pyslim/
Jun 5
Daiki Tagami
,
Ben Haller
5
May 31
Linux install without root
Dear Benjamin, Thank you very much for your reply, and this code runs very fast compared to the one
unread,
Linux install without root
Dear Benjamin, Thank you very much for your reply, and this code runs very fast compared to the one
May 31
Zuxi Cui
,
Ben Haller
5
May 25
Question about the randomization of mating
Sure. I'll play with 16.12 and reach back to you if I have further questions. Terry On Wed, May
unread,
Question about the randomization of mating
Sure. I'll play with 16.12 and reach back to you if I have further questions. Terry On Wed, May
May 25
Richard Sibly
,
Ben Haller
4
May 20
SLiM model of two alleles at a single locus
Hi folks, just a quick followup on this thread about writing biallelic models in SLiM. I've just
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SLiM model of two alleles at a single locus
Hi folks, just a quick followup on this thread about writing biallelic models in SLiM. I've just
May 20
bob
,
Ben Haller
5
May 14
number cycles set by variable?
ah, thanks again ben! sorry about that, i assumed that section only referred to the case of command
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number cycles set by variable?
ah, thanks again ben! sorry about that, i assumed that section only referred to the case of command
May 14
Thomas Birley
,
Ben Haller
2
May 12
Problems importing msprime
Hi Thomas, This is an msprime issue, not a SLiM issue, so you probably want to take it up with those
unread,
Problems importing msprime
Hi Thomas, This is an msprime issue, not a SLiM issue, so you probably want to take it up with those
May 12
Chrystelle Delord
, …
Peter Ralph
9
May 12
Recapitate a SLiM 3.6 tree into pyslim 0.700 with msprime.Demography(): metadata issue?
Thank you very much Peter! I am looking forward to using this solution in the future. I am very sorry
unread,
Recapitate a SLiM 3.6 tree into pyslim 0.700 with msprime.Demography(): metadata issue?
Thank you very much Peter! I am looking forward to using this solution in the future. I am very sorry
May 12
Roslyn Nolan
,
Ben Haller
6
May 11
population size less than expected in non-WF K/N model
Hi Roslyn. Perhaps I'm missing the point, but you can do whatever you want in script. :-> For
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population size less than expected in non-WF K/N model
Hi Roslyn. Perhaps I'm missing the point, but you can do whatever you want in script. :-> For
May 11
Bjarki Eldon
,
Ben Haller
3
May 10
dominant advantageous mutations
Hi Bjarki! Well, that is what this particular model does. :-> To see why, you can just run it in
unread,
dominant advantageous mutations
Hi Bjarki! Well, that is what this particular model does. :-> To see why, you can just run it in
May 10
Guillaume Lan-Fong
,
Ben Haller
4
May 9
Conditional sweep simulations with migration - broken RNG ? / saving migration rate / rescheduling event
Hello Ben, Thanks a lot for taking the time to read this huge mail, and to give some answers to my
unread,
Conditional sweep simulations with migration - broken RNG ? / saving migration rate / rescheduling event
Hello Ben, Thanks a lot for taking the time to read this huge mail, and to give some answers to my
May 9
Diego Salazar Tortosa
,
Ben Haller
4
May 7
Stack of mutations in non-nucleotide models
Thanks Diego! I have modified that paragraph in the manual to read: Positions 3, 5, and 10 in this
unread,
Stack of mutations in non-nucleotide models
Thanks Diego! I have modified that paragraph in the manual to read: Positions 3, 5, and 10 in this
May 7
Yujean Kim
,
Ben Haller
4
Apr 27
Prevention of outcrossing ability depending on the genotype of the individual
Hi Yujean. It looks like your script has a stray "return T;" in the modifyChild() callback
unread,
Prevention of outcrossing ability depending on the genotype of the individual
Hi Yujean. It looks like your script has a stray "return T;" in the modifyChild() callback
Apr 27
Richard Sibly
,
Ben Haller
7
Apr 12
output the number of mutations in each of two patches to a LogFile
Hi Richard, Sounds like removing unique() is getting you what you wanted; I guess I misunderstood
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output the number of mutations in each of two patches to a LogFile
Hi Richard, Sounds like removing unique() is getting you what you wanted; I guess I misunderstood
Apr 12
Anushka
, …
Ben Haller
9
Apr 12
Soft sweep simulation too slow
One more on-list reply for closure; follow up off-list as Peter suggested, please. So, to resolve the
unread,
Soft sweep simulation too slow
One more on-list reply for closure; follow up off-list as Peter suggested, please. So, to resolve the
Apr 12
Bjarki Eldon
, …
Ben Haller
7
Apr 11
nonWF simulation
Just a quick followup on this matter of the findInterval() function. It has just been added to Eidos,
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nonWF simulation
Just a quick followup on this matter of the findInterval() function. It has just been added to Eidos,
Apr 11
Guillaume Lan-Fong
,
Peter Ralph
4
Apr 8
Recapitation using specified demography
Hi, Guillaume! We should probably move further discussion off-list, but quick answers: > So here,
unread,
Recapitation using specified demography
Hi, Guillaume! We should probably move further discussion off-list, but quick answers: > So here,
Apr 8
Jeffrey Groh
, …
Jeff
3
Mar 31
reading rec map from file: slim complaining that ends not in ascending order - but they are?
Ah, OK this makes sense. Many thanks for spotting this which I should have seen myself! Cheers, Jeff
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reading rec map from file: slim complaining that ends not in ascending order - but they are?
Ah, OK this makes sense. Many thanks for spotting this which I should have seen myself! Cheers, Jeff
Mar 31
Bradburd
, …
Ben Haller
4
Mar 25
spatial interactions separated along "z" axis
Got it - thanks Ben & Peter! Gideon Bradburd (he/him) Dept. Integrative Biology Michigan State
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spatial interactions separated along "z" axis
Got it - thanks Ben & Peter! Gideon Bradburd (he/him) Dept. Integrative Biology Michigan State
Mar 25
Nathan Anderson
, …
Peter Ralph
8
Mar 21
Changing stacking policy in msprime.SLiMMutationModel(type=1)
Hi all Thank you for your suggestions. You're correct that the pipeline I've taken with
unread,
Changing stacking policy in msprime.SLiMMutationModel(type=1)
Hi all Thank you for your suggestions. You're correct that the pipeline I've taken with
Mar 21