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钱晓波
,
Ryan Gutenkunst
3
Apr 22
Confused with effective sequenced length (L)
Hello Xiaobo, I would go with option 3. Another (perhaps better) way to think of this is that what
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Confused with effective sequenced length (L)
Hello Xiaobo, I would go with option 3. Another (perhaps better) way to think of this is that what
Apr 22
Mathilde SALAMON
,
Ryan Gutenkunst
10
Apr 16
Out of memory boostrapping
Hi Ryan, that's what I suspected. I was able to generate the bootstraps SFS with your
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Out of memory boostrapping
Hi Ryan, that's what I suspected. I was able to generate the bootstraps SFS with your
Apr 16
Alex Hart
, …
Ryan Gutenkunst
9
Apr 11
trouble running neutral model
Hello Mario, Correct, if you can assume unlinked loci, you don't need to worry about composite
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trouble running neutral model
Hello Mario, Correct, if you can assume unlinked loci, you don't need to worry about composite
Apr 11
Daniel Portik
, …
Ryan Gutenkunst
5
Apr 8
Timing of discrete admixture events
Hello Diana, Your model code looks good to me. Here T2 would be the time in the past that the
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Timing of discrete admixture events
Hello Diana, Your model code looks good to me. Here T2 would be the time in the past that the
Apr 8
Mario Ernst
, …
Mario
3
Mar 29
1D frequency spectrum model data too low
If anyone is facing a similar issue, I wanted to share that I discovered the discrepancy was due to
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1D frequency spectrum model data too low
If anyone is facing a similar issue, I wanted to share that I discovered the discrepancy was due to
Mar 29
Chenlu Di
,
Ryan Gutenkunst
4
Mar 18
dadi-cli: fit DFE with neutral+gamma distribution
Hello Chenlu, I'm sorry I haven't been more responsive about this. I'm not sure what you
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dadi-cli: fit DFE with neutral+gamma distribution
Hello Chenlu, I'm sorry I haven't been more responsive about this. I'm not sure what you
Mar 18
Kasey Pham
,
Ryan Gutenkunst
3
Mar 15
Null distribution for Likelihood Ratio Testing
That's a big help, thank you! On Monday, March 11, 2024 at 5:52:48 PM UTC-4 Ryan Gutenkunst wrote
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Null distribution for Likelihood Ratio Testing
That's a big help, thank you! On Monday, March 11, 2024 at 5:52:48 PM UTC-4 Ryan Gutenkunst wrote
Mar 15
Ryan Gutenkunst
Mar 5
Re: [dadi-user] Defining complex demography
Hello Miles, The integration methods really define time intervals. So the integration will move the
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Re: [dadi-user] Defining complex demography
Hello Miles, The integration methods really define time intervals. So the integration will move the
Mar 5
Zoe Meziere
,
Ryan Gutenkunst
9
Mar 5
NAN confidence intervals FIM
Great, thank you very much for you help Ryan! Best, Zoe On Monday 4 March 2024 at 13:12:54 UTC+10
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NAN confidence intervals FIM
Great, thank you very much for you help Ryan! Best, Zoe On Monday 4 March 2024 at 13:12:54 UTC+10
Mar 5
Miles Anderson
,
Ryan Gutenkunst
2
Feb 25
Interpreting residuals
Hello Miles, Your interpretation of the residual plot is correct. I agree the other portions of the
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Interpreting residuals
Hello Miles, Your interpretation of the residual plot is correct. I agree the other portions of the
Feb 25
Tahir Ali
,
Ryan Gutenkunst
2
Feb 25
How can I estimate the unfolded 2D SFS using dadi or any other tool?
Hello Tahir, My postdoc David Castellano (CC'd) explored using the est-sfs method for his
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How can I estimate the unfolded 2D SFS using dadi or any other tool?
Hello Tahir, My postdoc David Castellano (CC'd) explored using the est-sfs method for his
Feb 25
Katharine Prata
,
Ryan Gutenkunst
3
Feb 16
Apparent excess of mid-frequency alleles in 1d-spectrum
Hello Kat, With folded spectra, the ancestral state doesn't matter at all, so I'm surprised
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Apparent excess of mid-frequency alleles in 1d-spectrum
Hello Kat, With folded spectra, the ancestral state doesn't matter at all, so I'm surprised
Feb 16
Miles Anderson
,
Ryan Gutenkunst
2
Feb 13
VCF polarization
Hi Miles, If you're already modifying the VCF file, the easiest way is to set the “AA=“ INFO flag
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VCF polarization
Hi Miles, If you're already modifying the VCF file, the easiest way is to set the “AA=“ INFO flag
Feb 13
Suany Quesada
,
Ryan Gutenkunst
4
12/6/23
Problem with running dadi with SNP panel data.
Hello Suany, My apologies, I made an important typo. SNP panel data are generally *unsuitable* for
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Problem with running dadi with SNP panel data.
Hello Suany, My apologies, I made an important typo. SNP panel data are generally *unsuitable* for
12/6/23
David Dayan
,
Suany Quesada
2
12/6/23
Stretching Data Suitability
Hello. Were you able to solve your question? I have a similar situation. I have a problem with
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Stretching Data Suitability
Hello. Were you able to solve your question? I have a similar situation. I have a problem with
12/6/23
David Bass
,
Ryan Gutenkunst
2
10/26/23
Setting relative bounds
Hello David, Using the dadi.Inference.opt method, which is a wrapper around NLopt, you can specify
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Setting relative bounds
Hello David, Using the dadi.Inference.opt method, which is a wrapper around NLopt, you can specify
10/26/23
Mario Ernst
,
Ryan Gutenkunst
2
10/16/23
troubleshooting poor visual fit
Hello Mario, I agree that the fit seems relatively poor, particularly private alleles in population 1
unread,
troubleshooting poor visual fit
Hello Mario, I agree that the fit seems relatively poor, particularly private alleles in population 1
10/16/23
Mario Ernst
,
Ryan Gutenkunst
3
10/16/23
modeling the split between non-sister populations?
Thanks for the answer! That's a good point. I will keep it in mind. Ryan Gutenkunst schrieb am
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modeling the split between non-sister populations?
Thanks for the answer! That's a good point. I will keep it in mind. Ryan Gutenkunst schrieb am
10/16/23
Chenlu Di
,
Ryan Gutenkunst
2
10/8/23
dadi.Inference.opt
Hello Chenlu, It's actually imported from dadi.NLopt_mod: https://dadi.readthedocs.io/en/latest/
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dadi.Inference.opt
Hello Chenlu, It's actually imported from dadi.NLopt_mod: https://dadi.readthedocs.io/en/latest/
10/8/23
Alex Krohn
,
Ryan Gutenkunst
5
9/29/23
Power With Low SNPs and High Numbers of Individuals
Thanks again for the suggestions. I really appreciate the guidance. -Alex On Thu, Sep 28, 2023 at 7:
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Power With Low SNPs and High Numbers of Individuals
Thanks again for the suggestions. I really appreciate the guidance. -Alex On Thu, Sep 28, 2023 at 7:
9/29/23
chichi zhao
,
Ryan Gutenkunst
2
9/19/23
Make_plots.py problems
Hello Chichi, You're using the Portik pipeline it appears, which I'm not familiar with all
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Make_plots.py problems
Hello Chichi, You're using the Portik pipeline it appears, which I'm not familiar with all
9/19/23
Mathilde SALAMON
,
Ryan Gutenkunst
3
9/4/23
Precision population name order import SNP data format pop_ids model
Hello Ryan, thank you for your answer, this was very useful. Best wishes, Mathilde Le samedi 19 août
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Precision population name order import SNP data format pop_ids model
Hello Ryan, thank you for your answer, this was very useful. Best wishes, Mathilde Le samedi 19 août
9/4/23
Panos Zerv
,
Ryan Gutenkunst
2
8/24/23
Split and bottleneck model
Hello Panagiotis, 1. Mis-modeled recent demographic events can bias the inference of older events. 2.
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Split and bottleneck model
Hello Panagiotis, 1. Mis-modeled recent demographic events can bias the inference of older events. 2.
8/24/23
Zoe Meziere
, …
Travis Struck
4
8/23/23
dadi-cli --global-optimization outputs theta = 0.0
Great, thanks a lot Travis! On Thursday, 24 August 2023 at 10:16:52 UTC+10 Travis Struck wrote: Hi
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dadi-cli --global-optimization outputs theta = 0.0
Great, thanks a lot Travis! On Thursday, 24 August 2023 at 10:16:52 UTC+10 Travis Struck wrote: Hi
8/23/23
Juan Manuel Gorospe Ballesteros
, …
Ryan Gutenkunst
4
8/23/23
demographic modeling of high polyploid populations
Hello Juan, In general, any demographic history model will be a crude approximation to the complex
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demographic modeling of high polyploid populations
Hello Juan, In general, any demographic history model will be a crude approximation to the complex
8/23/23
Nemo Wu
,
Ryan Gutenkunst
8
8/1/23
dadi analysis for selfing plant
Hi, Ryan, Thank you!you really help me a lot. Best Ryan Gutenkunst <rgute...@gmail.com> 于
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dadi analysis for selfing plant
Hi, Ryan, Thank you!you really help me a lot. Best Ryan Gutenkunst <rgute...@gmail.com> 于
8/1/23
Tanya Welgemoed
, …
Travis Struck
4
8/1/23
Cython compilation error
Hi Tanya, I've updated the dadi source code on bitbucket, so you, and anyone else using the
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Cython compilation error
Hi Tanya, I've updated the dadi source code on bitbucket, so you, and anyone else using the
8/1/23
Jen Lain
,
Ryan Gutenkunst
2
7/25/23
Plotting DFE
Hello Jen, This functionality isn't built into dadi. You can use your favorite plotting program (
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Plotting DFE
Hello Jen, This functionality isn't built into dadi. You can use your favorite plotting program (
7/25/23
Sam Donohoo
,
Ryan Gutenkunst
2
7/10/23
Ratio and Theta Definition Question
Hello Sam, Sorry for the slow reply. I've been out for our 4th of July holiday. Responds below.
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Ratio and Theta Definition Question
Hello Sam, Sorry for the slow reply. I've been out for our 4th of July holiday. Responds below.
7/10/23
Aude Caizergues
, …
Qi Fu
9
5/9/23
RAD-seq data and L
Hi Ryan, Thank you for your comments. I greatly appreciate your help! Best, Qi 在2023年5月10日星期三 UTC+8
unread,
RAD-seq data and L
Hi Ryan, Thank you for your comments. I greatly appreciate your help! Best, Qi 在2023年5月10日星期三 UTC+8
5/9/23