slim-discuss

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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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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

Ornob Alam, Ben Haller2

Jun 30

Parametrizing generation times and adding conditional arguments for abc

Hi! I can't really debug people's models for them on slim-discuss; with hundreds of users of

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Parametrizing generation times and adding conditional arguments for abc

Hi! I can't really debug people's models for them on slim-discuss; with hundreds of users of

Jun 30

Stella Knief, Ben Haller3

Jun 30

Fitness Error and Bounded Distributions in SLiM

Hi Ben, Thank you so much! The new script is working beautifully, and the nested if-else statements

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Fitness Error and Bounded Distributions in SLiM

Hi Ben, Thank you so much! The new script is working beautifully, and the nested if-else statements

Jun 30

Matthias Steinrücken, Ben Haller3

Jun 29

Copy genomes

Hi Benjamin, Thanks a bunch for the quick reply. I think your suggested code snippet will do exactly

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Copy genomes

Hi Benjamin, Thanks a bunch for the quick reply. I think your suggested code snippet will do exactly

Jun 29

Suhail Ghafoor, Ben Haller2

Jun 27

Implementing custom mutation matrix

Hi! I'm not sure what you mean by "1x96 form". However, I think the explanation for

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Implementing custom mutation matrix

Hi! I'm not sure what you mean by "1x96 form". However, I think the explanation for

Jun 27

Dan Schrider, Ben Haller3

Jun 24

Times to fixation and loss

Thanks Ben! That looks great, and we will compare to the GUI's histograms just to confirm and let

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Times to fixation and loss

Thanks Ben! That looks great, and we will compare to the GUI's histograms just to confirm and let

Jun 24

bcar...@mtroyal.ca, Ben Haller3

Jun 16

writeFile Stream Errors

Woopsie. Gotta love HPC. I was using a folder where the CGROUP is disk quota is full. Filled up a 1T

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writeFile Stream Errors

Woopsie. Gotta love HPC. I was using a folder where the CGROUP is disk quota is full. Filled up a 1T

Jun 16

Bernard Kim, … bcar...@mtroyal.ca21

Jun 14

SLiM GUI running natively on Microsoft Windows 10 with WSL

Ah, a fellow Emacs user! :) That's really cool that Microsoft is making it easier to use more and

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SLiM GUI running natively on Microsoft Windows 10 with WSL

Ah, a fellow Emacs user! :) That's really cool that Microsoft is making it easier to use more and

Jun 14

Christopher McAllester, … bcar...@mtroyal.ca3

Jun 14

Sublime Text 3+ syntax/commenting/code highlights for SLiM

That's really interesting. If I knew enough C++ or Qt, I would "extract" the

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Sublime Text 3+ syntax/commenting/code highlights for SLiM

That's really interesting. If I knew enough C++ or Qt, I would "extract" the

Jun 14

Peter Ralph

Jun 14

Re: pyslim VCF output nonconforming when reading treeseq

Follow-up here (I replied off-list, whoops): The problem is that - the ALT allele you're seeing

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Re: pyslim VCF output nonconforming when reading treeseq

Follow-up here (I replied off-list, whoops): The problem is that - the ALT allele you're seeing

Jun 14

Soumitra Bhide, Ben Haller2

Jun 14

Hibernation

Hi Soumitra! Hmm, well, here are a couple of thoughts: - If you really want "every aspect of the

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Hibernation

Hi Soumitra! Hmm, well, here are a couple of thoughts: - If you really want "every aspect of the

Jun 14

Jay, Ben Haller2

Jun 10

cloning rate algorithm and identifying the number of clones

Hi John! As you've realized, in the default Wright-Fisher (WF) model type in SLiM the cloning

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cloning rate algorithm and identifying the number of clones

Hi John! As you've realized, in the default Wright-Fisher (WF) model type in SLiM the cloning

Jun 10