slim-discuss

1–30 of 457

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 Ralph3

Jun 29

Errors with pyslim.recapitate( )

Hi, Kadee! Let's see: there's some kind of mismatch between where the lineages are in the

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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 Haller2

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

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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 Haller2

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 Haller4

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

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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 Haller6

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 Haller8

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!

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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

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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 Ralph4

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

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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 Ralph2

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 Haller2

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

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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

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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 Ralph2

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 Haller5

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

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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 Haller5

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

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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 Haller4

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 Haller5

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 Haller2

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

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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 Ralph9

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

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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 Haller6

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 Haller3

May 10

dominant advantageous mutations

Hi Bjarki! Well, that is what this particular model does. :-> To see why, you can just run it in

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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 Haller4

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

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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 Haller4

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

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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 Haller4

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

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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 Haller7

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 Haller9

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

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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 Haller7

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 Ralph4

Apr 8

Recapitation using specified demography

Hi, Guillaume! We should probably move further discussion off-list, but quick answers: > So here,

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Recapitation using specified demography

Hi, Guillaume! We should probably move further discussion off-list, but quick answers: > So here,

Apr 8

Jeffrey Groh, … Jeff3

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 Haller4

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 Ralph8

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

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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