slim-discuss

1–30 of 403

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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bob, Ben Haller2

Dec 3

possible to output two tree sequences?

SLiM can only output the tree sequence for the whole simulation, but you should be able to just

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possible to output two tree sequences?

SLiM can only output the tree sequence for the whole simulation, but you should be able to just

Dec 3

Guillaume Lan-Fong, Miguel de Navascués4

Nov 24

Underestimate of Fis - Adding a set number of SNP

Hi Guillaume, It might not be very intuitive but Fis does not get quickly to the equilibrium state.

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Underestimate of Fis - Adding a set number of SNP

Hi Guillaume, It might not be very intuitive but Fis does not get quickly to the equilibrium state.

Nov 24

Chase W. Nelson, … Ben Haller5

Nov 23

Including originalNuc in output & efficiently counting nucleotides at a position

Dear Ben and Peter: You're both simply wonderful — this is perfect! Because my model outputs

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Including originalNuc in output & efficiently counting nucleotides at a position

Dear Ben and Peter: You're both simply wonderful — this is perfect! Because my model outputs

Nov 23

Guillaume Lan-Fong, … Peter Ralph8

Nov 22

Recapitation with recombination map ends with multiple roots

Thanks to both of you for your detailled answers and your advices :) Cheers, G. LF Le mardi 16

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Recapitation with recombination map ends with multiple roots

Thanks to both of you for your detailled answers and your advices :) Cheers, G. LF Le mardi 16

Nov 22

Jason de Koning, … andrea mrnjavac7

Nov 16

strange behaviour when modelling recurrent mutation

Hi Ben, thank you for the explanation. I was experiencing "logjam" and managed to fix it by

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strange behaviour when modelling recurrent mutation

Hi Ben, thank you for the explanation. I was experiencing "logjam" and managed to fix it by

Nov 16

Nick O'Brien, … Ben Haller4

Nov 10

Coalescent burn-in advice

Hi Ben and Miguel, Thank you for your comments! I've tried out the GitHub head and it seems to be

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Coalescent burn-in advice

Hi Ben and Miguel, Thank you for your comments! I've tried out the GitHub head and it seems to be

Nov 10

font...@gmail.com, Ben Haller3

Nov 3

Problems compiling SLiM on Ubuntu 21.10

Hi Ben, Just compiled from git and it works on Ubuntu 21.10 Cheers JP On Wednesday, November 3, 2021

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Problems compiling SLiM on Ubuntu 21.10

Hi Ben, Just compiled from git and it works on Ubuntu 21.10 Cheers JP On Wednesday, November 3, 2021

Nov 3

Julien Y. Dutheil, … Jose Luis Mijangos6

Nov 3

Realistic background selection

Dear Luis, Thank you very much for the insights! This sounds like a plausible mechanism, but I would

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Realistic background selection

Dear Luis, Thank you very much for the insights! This sounds like a plausible mechanism, but I would

Nov 3

Chase W. Nelson2

Nov 2

Does .output() report sites that differ from the ancestral sequence but lack polymorphism in the sample?

Further apologies for the clutter; I have answered my own question and the answer is 'yes'!

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Does .output() report sites that differ from the ancestral sequence but lack polymorphism in the sample?

Further apologies for the clutter; I have answered my own question and the answer is 'yes'!

Nov 2

Olivia Johnson, Ben Haller4

Oct 27

Offspring Number Capping

Thank you for this! I will download the GitHub version and give it a go! Thanks Olivia On Wednesday,

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Offspring Number Capping

Thank you for this! I will download the GitHub version and give it a go! Thanks Olivia On Wednesday,

Oct 27

Anita Lerch, Ben Haller2

Oct 26

Individual survive iteration even with fitnessScaling set to 0

Hi Anita. I'd need to see your model to diagnose this problem. Please post your model's code,

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Individual survive iteration even with fitnessScaling set to 0

Hi Anita. I'd need to see your model to diagnose this problem. Please post your model's code,

Oct 26

Xiong, Tianzhu, Ben Haller2

Oct 14

Ways to suppress "migration arrows" in population visualization?

Hi Tianzhu! There isn't right now, but it would be easy to add. I'll put it on my to do list,

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Ways to suppress "migration arrows" in population visualization?

Hi Tianzhu! There isn't right now, but it would be easy to add. I'll put it on my to do list,

Oct 14

Chase W. Nelson, Ben Haller4

Oct 4

Can -s/setSeed() be given a value that does not change the seed?

Thank you so much! This solution works perfectly, with -d "NULL" being interpreted as the

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Can -s/setSeed() be given a value that does not change the seed?

Thank you so much! This solution works perfectly, with -d "NULL" being interpreted as the

Oct 4

Tom McMahon, … Chrystelle Delord7

Sep 30

Serial sampling and tree sequences

Hi Peter, Thank you very much, that helps a lot! I figured out I had been missing a few things: I

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Serial sampling and tree sequences

Hi Peter, Thank you very much, that helps a lot! I figured out I had been missing a few things: I

Sep 30

hern....@gmail.com, … Peter Ralph6

Sep 27

Questions about treeseq good practices

Hi, Hernán - thanks for reporting back! A few notes: > (1) running the simulation with slim -

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Questions about treeseq good practices

Hi, Hernán - thanks for reporting back! A few notes: > (1) running the simulation with slim -

Sep 27

Jon Lerga Jaso, … Zuxi Cui3

Sep 21

Simulate a large European population / issue with outputVCFSample?

Jon, I have been doing something similar now and it is possible to simulate up to 10K independent

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Simulate a large European population / issue with outputVCFSample?

Jon, I have been doing something similar now and it is possible to simulate up to 10K independent

Sep 21

Yaniv Brandvain, … Yaniv Brandvain9

Sep 10

Calculating inbreeding depression

Thanks Chris, I'll have a look and a think about this!My first thought was to turn to your github

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Calculating inbreeding depression

Thanks Chris, I'll have a look and a think about this!My first thought was to turn to your github

Sep 10

Nkrumah Grant, Ben Haller3

Aug 29

Saving output

Wow, thank you so much. Easy fix. On Sun, Aug 29, 2021 at 11:07 AM 'Ben Haller' via slim-

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Saving output

Wow, thank you so much. Easy fix. On Sun, Aug 29, 2021 at 11:07 AM 'Ben Haller' via slim-

Aug 29

font...@gmail.com, Peter Ralph2

Aug 25

Interpreting spatial interaction and simulated landscape values

Hi, JP - good questions: > Lets assume an example where I initiate a simulation with

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Interpreting spatial interaction and simulated landscape values

Hi, JP - good questions: > Lets assume an example where I initiate a simulation with

Aug 25

Soumitra Bhide, … r.di...@gmail.com6

Aug 24

Extracting Spatital Dynamics of the simulation as a video file

Hi Soumitra, You can also accomplish this using my new R package {slimr}. I just whipped up a minimal

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Extracting Spatital Dynamics of the simulation as a video file

Hi Soumitra, You can also accomplish this using my new R package {slimr}. I just whipped up a minimal

Aug 24

Zuxi Cui, Ben Haller3

Aug 20

Having an issue with nucleotide-base simulation

Hi all, Ben helped me with the debug and we found the potential causes of the issue are tri-allelic

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Having an issue with nucleotide-base simulation

Hi all, Ben helped me with the debug and we found the potential causes of the issue are tri-allelic

Aug 20

Nkrumah Grant, Ben Haller2

Aug 12

Population size causing simulation to finish before N_generations have completed

Hi Nkrumah! Nice catch. This was actually caused by three different bugs, each of which was pretty

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Population size causing simulation to finish before N_generations have completed

Hi Nkrumah! Nice catch. This was actually caused by three different bugs, each of which was pretty

Aug 12

Yujean Kim, Ben Haller2

Aug 12

Saving results into a tsv file

Hi Yujean. There are several issues here. See section 4.2.5 of the SLiM manual for an example of how

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Saving results into a tsv file

Hi Yujean. There are several issues here. See section 4.2.5 of the SLiM manual for an example of how

Aug 12

Yujean Kim, Jackson Champer2

Aug 9

Modelling different gene drive scenarios on snails to prevent schistosomiasis

The "intrinsic growth rate" for a discrete generation model should not be below 1, or else

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Modelling different gene drive scenarios on snails to prevent schistosomiasis

The "intrinsic growth rate" for a discrete generation model should not be below 1, or else

Aug 9

Tristan Dennis, … Peter Ralph6

Aug 6

Highest density point

Ah! Got it, thanks very much for your help Peter! Tristan On Tuesday, August 3, 2021 at 7:33:57 PM

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Highest density point

Ah! Got it, thanks very much for your help Peter! Tristan On Tuesday, August 3, 2021 at 7:33:57 PM

Aug 6

Yujean Kim, … Sam Champer3

Aug 5

Sublaunching SLiM in R

I must admit that I run SLiM from python much more often than I do from R! As Ben mentioned, the

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Sublaunching SLiM in R

I must admit that I run SLiM from python much more often than I do from R! As Ben mentioned, the

Aug 5

Ornob Alam, Philipp Messer3

Jul 30

Rescaling a selection coefficient

Dear Philipp, Thanks, that does help. I am going to try it with a couple of different quantities.

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Rescaling a selection coefficient

Dear Philipp, Thanks, that does help. I am going to try it with a couple of different quantities.

Jul 30

Xiong, Tianzhu, Peter Ralph4

Jul 15

pyslim tree_sequence's "individual_populations" does not equal individual's population record in metadata

> Regarding this, will the method described in the tutorial for sampling individuals from multiple

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pyslim tree_sequence's "individual_populations" does not equal individual's population record in metadata

> Regarding this, will the method described in the tutorial for sampling individuals from multiple

Jul 15

Nathan Anderson, Ben Haller5

Jul 13

Mirroring Sequence of Events in an Evolve and Resequence Experiment

Hi Ben I think I understand now, your explanations were very helpful. Thanks for your help! Nathan On

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Mirroring Sequence of Events in an Evolve and Resequence Experiment

Hi Ben I think I understand now, your explanations were very helpful. Thanks for your help! Nathan On

Jul 13

Greg Torda, Peter Ralph3

Jul 10

pyslim - calculating mean tree height for subset of individuals

This is it, thanks heaps for the prompt reply, Peter! Here is what I did (in case anyone was

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pyslim - calculating mean tree height for subset of individuals

This is it, thanks heaps for the prompt reply, Peter! Here is what I did (in case anyone was

Jul 10