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Welcome to the discussion group on fastsimcoal2

The program fastsimcoal2 allows one to simulate genetic and genomic data under complex evolutionary models using a fast sequential Markov coalescent simulation framework, and to estimate demographic parameters from complex evolutionary models from the (joint) site frequency spectrum
More information about the software, a user manual, and executable versions for windows, mac OSX and linux can be found on http://cmpg.unibe.ch/software/fastsimcoal2

A NEW VERSION OF FASTSIMCOAL2 (VER 2.8.0) IS NOW AVAILABLE (16 October 2023)

fsc28 offers the ability to deal with sample spatial and time heterogeneity with the introduction of the notion of sfs pools

Please download the new version on http://cmpg.unibe.ch/software/fastsimcoal2/

0 selected

Laurent Excoffier, … Nicolai Nuerk3

10/29/19

new par file interpreter ver 6.3

(maybe outdated but…) it's on the fastsimcoal2 web page under 'visualizing scenarios modeld

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new par file interpreter ver 6.3

(maybe outdated but…) it's on the fastsimcoal2 web page under 'visualizing scenarios modeld

10/29/19

Laurent Excoffier, peace.wa...@gmail.com2

10/31/17

New version of fastsimcoal2 (ver 2.6)

Dear Laurent, I do not quite understand the option "--foldedSFS". Does that means I could

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New version of fastsimcoal2 (ver 2.6)

Dear Laurent, I do not quite understand the option "--foldedSFS". Does that means I could

10/31/17

DiedeMaas, … Sarah Wells8

Sep 2

Simple bottleneck model folded SFS

Just thought I would reply to this thread as I see this issue has come up multiple times with no

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Simple bottleneck model folded SFS

Just thought I would reply to this thread as I see this issue has come up multiple times with no

Sep 2

Ryan N Gutenkunst

Aug 25

Compete in GHIST - the Genomic History Inference Strategies Tournament

Hello fastsimcoal2 users! The 2025 Genomic History Inference Strategies Tournament (GHIST) is live at

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Compete in GHIST - the Genomic History Inference Strategies Tournament

Hello fastsimcoal2 users! The 2025 Genomic History Inference Strategies Tournament (GHIST) is live at

Aug 25

Aug 5

Questions about population size

Dear Prof. Exoffier and everyone in google group, I'm using fsc2 to infer the population history

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Questions about population size

Dear Prof. Exoffier and everyone in google group, I'm using fsc2 to infer the population history

Aug 5

Vincent Kendlbacher

Jul 30

Error when using paramInRange

Dear all, I am having a very hard time getting my tpl & est files to run. The tpl. file is the

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Error when using paramInRange

Dear all, I am having a very hard time getting my tpl & est files to run. The tpl. file is the

Jul 30

Jul 10

Population Genomics Using Ancient DNA Data

Dear all, We are excited to announce our upcoming Physalia online course: Population Genomics Using

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Population Genomics Using Ancient DNA Data

Dear all, We are excited to announce our upcoming Physalia online course: Population Genomics Using

Jul 10

Ancient Population Genomics IBE

Jul 10

Different recombination rates and/or landscapes

I am a loyal FSC user, and I want to simulate two sister populations with different recombination

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Different recombination rates and/or landscapes

I am a loyal FSC user, and I want to simulate two sister populations with different recombination

Jul 10

Jul 8

Is using -S option vs -d0 option with same seed number doing the same underlying simulation?

Hi all, I'm testing statistical properties of fastsimcoal vs another software which requires full

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Is using -S option vs -d0 option with same seed number doing the same underlying simulation?

Hi all, I'm testing statistical properties of fastsimcoal vs another software which requires full

Jul 8

Coleen, Laurent Excoffier3

Jun 10

MRCA not found!

Hi, Laurent Thank you very much for your prompt reply. Even after adding "paramInRange",

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MRCA not found!

Hi, Laurent Thank you very much for your prompt reply. Even after adding "paramInRange",

Jun 10

Hari Shankar Gadri

May 22

demography analysis from fsc28

Subject: Using EasySFS .obs File with fastsimcoal2 (fsc28) Dear Developer, I hope this message finds

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demography analysis from fsc28

Subject: Using EasySFS .obs File with fastsimcoal2 (fsc28) Dear Developer, I hope this message finds

May 22

Luz Elena De la Ossa

May 19

Error: Segmentation fault (core dumped)

Dear Laurent and fastsimcoal users, I am new to this program and am facing some difficulties. I am

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Error: Segmentation fault (core dumped)

Dear Laurent and fastsimcoal users, I am new to this program and am facing some difficulties. I am

May 19

Mar 28

How to compute the 95% confidence intervals?

Dear Laurent and fastsimcoal users, I have already completed bootstrapping parameters for my chosen

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How to compute the 95% confidence intervals?

Dear Laurent and fastsimcoal users, I have already completed bootstrapping parameters for my chosen

Mar 28

Mar 24

Please help a new user identify mistakes

Hello everyone, I am a new user of fastsimcoal2. After studying the user manual, I have attempted to

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Please help a new user identify mistakes

Hello everyone, I am a new user of fastsimcoal2. After studying the user manual, I have attempted to

Mar 24

Mar 21

Estimation from SFS; tpl error extinct deme

Hello and thank you for any help! I am trying to perform demographic inference from the SFS and am

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Estimation from SFS; tpl error extinct deme

Hello and thank you for any help! I am trying to perform demographic inference from the SFS and am

Mar 21

Mar 10

Calculating Akaike Weights for best fitting models

We're testing some models for a population which went through recent and short bottlenecks. Our

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Calculating Akaike Weights for best fitting models

We're testing some models for a population which went through recent and short bottlenecks. Our

Mar 10

Tim, Laurent Excoffier4

Jan 26

fastsimcoal28 not generating likelihoods

Dear Laurent, Thanks a ton! You made it work! The file extensions were of course correct in the

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fastsimcoal28 not generating likelihoods

Dear Laurent, Thanks a ton! You made it work! The file extensions were of course correct in the

Jan 26

Vicente Castillo, … yy Wu3

Jan 10

Parametric bootstrap

I wonder if it's normal to have only one build file *_boot_1.simparam when running bootstrap?

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Parametric bootstrap

I wonder if it's normal to have only one build file *_boot_1.simparam when running bootstrap?

Jan 10

Jie Gao, … yy Wu3

Jan 10

Problem of the simluation with best model

I wonder if it's normal to have only one build file *_boot_1.simparam when running bootstrap?

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Problem of the simluation with best model

I wonder if it's normal to have only one build file *_boot_1.simparam when running bootstrap?

Jan 10

Jeremy Davis, … Laurent Excoffier3

Jan 8

likelihoods always 0.000

Hi, it seems as if your obs file is not properly formatted (Missing header). Have a look at the

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likelihoods always 0.000

Hi, it seems as if your obs file is not properly formatted (Missing header). Have a look at the

Jan 8

aurelle...@gmail.com

12/14/24

heterozygote excess while simulating SNPs

Dear Laurent I use fsc28 to simulate some SNPs, similar to RADSeq data. I tried the following

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heterozygote excess while simulating SNPs

Dear Laurent I use fsc28 to simulate some SNPs, similar to RADSeq data. I tried the following

12/14/24

12/3/24

Simulations did not converge. MRCA not found!

I am using this command line: ./fsc28 -t model3.tpl -e model3.est -u model3_MSFS.obs -n 100000 -M -C

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Simulations did not converge. MRCA not found!

I am using this command line: ./fsc28 -t model3.tpl -e model3.est -u model3_MSFS.obs -n 100000 -M -C

12/3/24

Yasuto ISHII, Laurent Excoffier2

11/28/24

Linked SNPs and parameter estimation

Hi, On Thursday, 28 November 2024 at 03:34:03 UTC+1 y.ishii wrote: Dear Dr. Excoffier, I hope this

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Linked SNPs and parameter estimation

Hi, On Thursday, 28 November 2024 at 03:34:03 UTC+1 y.ishii wrote: Dear Dr. Excoffier, I hope this

11/28/24

11/15/24

Possible bug of a pv file

Dear Laurent and fastsimcoal2 developers, Thank you for developing and maintaining the excellent

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Possible bug of a pv file

Dear Laurent and fastsimcoal2 developers, Thank you for developing and maintaining the excellent

11/15/24

Rodrigo Francisco Justino

9/30/24

How to estimate migration rates with microsatellite genotyping data similar to those obtained from output files with .bestlhoods extension obtained from SFS of SNPs?

How to estimate migration rates with microsatellite genotyping data similar to those obtained from

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How to estimate migration rates with microsatellite genotyping data similar to those obtained from output files with .bestlhoods extension obtained from SFS of SNPs?

How to estimate migration rates with microsatellite genotyping data similar to those obtained from

9/30/24

岳亮, Beatriz Portinha2

9/11/24

Failure in running fsc28

Hi, In case you are still struggling with this, you need to make the "fsc28" file

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Failure in running fsc28

Hi, In case you are still struggling with this, you need to make the "fsc28" file

9/11/24

Ryan N Gutenkunst

8/30/24

Compete in GHIST - the Genomic History Inference Strategies Tournament

Hello fastsimcoal2 users! I encourage you to participate in GHIST, the Genomic History Inference

unread,

Compete in GHIST - the Genomic History Inference Strategies Tournament

Hello fastsimcoal2 users! I encourage you to participate in GHIST, the Genomic History Inference

8/30/24

yan peng, yulu ye2

8/27/24

Gene flow and introgression rates

hi, yan peng, Did you understand the question, I've just started simulating introgression with

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Gene flow and introgression rates

hi, yan peng, Did you understand the question, I've just started simulating introgression with

8/27/24

8/27/24

How to write about historical events in .tpl

Hi everyone, I want to describe a topology like this and I don't know if this is the right way to

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How to write about historical events in .tpl

Hi everyone, I want to describe a topology like this and I don't know if this is the right way to

8/27/24

8/21/24

Testing for simple population branching - No output produced

Dear users, I am having problems running a simple analysis perhaps someone can help here. I am using

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Testing for simple population branching - No output produced

Dear users, I am having problems running a simple analysis perhaps someone can help here. I am using

8/21/24

8/14/24

Rescaling factor changes with ECM cycles

Dear fastsimcoal users, I observed that when increasing the number of ECM cycles, in my case from -

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Rescaling factor changes with ECM cycles

Dear fastsimcoal users, I observed that when increasing the number of ECM cycles, in my case from -

8/14/24

Mario Erandi Bonillas-Monge

8/1/24

Testing for rapid growth of a deme with larger ancestral population

Hi Fsc2 team, I managed to run several models to calculate the divergence times and migration between

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Testing for rapid growth of a deme with larger ancestral population

Hi Fsc2 team, I managed to run several models to calculate the divergence times and migration between

8/1/24

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