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Alexander Klassmann
, …
Gabriele Nocchi
8
9/7/22
SweeD does not report correct CLR for folded spectra
Dear Pavlos, Has this bug been fixed? Gabriele On Friday, September 18, 2020 at 12:17:45 PM UTC+2
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SweeD does not report correct CLR for folded spectra
Dear Pavlos, Has this bug been fixed? Gabriele On Friday, September 18, 2020 at 12:17:45 PM UTC+2
9/7/22
Anik Du
6/24/22
SweeD selection sweep regions per populations
Hi Pavlos, Thank you very much for developing SweeD. I am running SweeD on individual chromosome with
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SweeD selection sweep regions per populations
Hi Pavlos, Thank you very much for developing SweeD. I am running SweeD on individual chromosome with
6/24/22
demetris taliadoros
, …
Nikolaos Alachiotis
8
5/9/22
RaisD and the sfs_code2ms converter
Hello Masha, I checked your file and there are monomorphic columns. RAiSD assumes that ms files do
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RaisD and the sfs_code2ms converter
Hello Masha, I checked your file and there are monomorphic columns. RAiSD assumes that ms files do
5/9/22
Brian Mack
, …
tou wowo
14
4/19/22
SweeD error - number of nucleotides
Thank you very much for your last reply. I used the VCF - Validator and got the following results. I
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SweeD error - number of nucleotides
Thank you very much for your last reply. I used the VCF - Validator and got the following results. I
4/19/22
Ymberzal Koul
1/21/22
Help
Hello, I am using vcf files to run SweeD on whole genome data. My vcf file contains * at some places
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Help
Hello, I am using vcf files to run SweeD on whole genome data. My vcf file contains * at some places
1/21/22
Brian Arnold
, …
Peter Civáň
7
6/28/21
using precomputed SweeD SFS for sweep scan
Hi Nikos, Thanks a lot for your help! I can confirm that using the -strictPolymorphic option for both
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using precomputed SweeD SFS for sweep scan
Hi Nikos, Thanks a lot for your help! I can confirm that using the -strictPolymorphic option for both
6/28/21
Karine Durand
,
N.Alachiotis
2
10/12/20
perl script to encode vcf in sweep finder format
This assertion suggests that there is something wrong with the input file rather than SweeD. More
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perl script to encode vcf in sweep finder format
This assertion suggests that there is something wrong with the input file rather than SweeD. More
10/12/20
Gab Diesel
,
N.Alachiotis
2
10/12/20
SweeD: different grid sizes give different results
Changing the grid size should not be affecting the results. It's mostly a matter of how you
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SweeD: different grid sizes give different results
Changing the grid size should not be affecting the results. It's mostly a matter of how you
10/12/20
Vlatko Galic
,
N.Alachiotis
2
10/12/20
RAiSD and SNP array data
You can find a response to this question here: https://github.com/alachins/raisd/issues/23 On Tuesday
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RAiSD and SNP array data
You can find a response to this question here: https://github.com/alachins/raisd/issues/23 On Tuesday
10/12/20
kevin sartori
9/28/20
Markovian Coalescent Simulator
Hi, thanks for sharing your tools and this discussion platform I'm studying the evolution of
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Markovian Coalescent Simulator
Hi, thanks for sharing your tools and this discussion platform I'm studying the evolution of
9/28/20
manas...@gmail.com
7/2/20
SweeD is running only for 1 chromosome
Hello Group, Am trying to run SweeD for my Rice Data of 226 Genotypes. may be my commands are wrong,
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SweeD is running only for 1 chromosome
Hello Group, Am trying to run SweeD for my Rice Data of 226 Genotypes. may be my commands are wrong,
7/2/20
Pavlos Pavlidis
, …
N.Alachiotis
6
6/30/20
Re: SweeD / OmegaPlus visualisation script
What I am trying to say is that we do not have access to those scripts on those servers anymore. Part
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Re: SweeD / OmegaPlus visualisation script
What I am trying to say is that we do not have access to those scripts on those servers anymore. Part
6/30/20
Brian Mack
,
Nikolaos Alachiotis
2
6/3/20
Should haplotypes or primitive SNPs be used for RAiSD input?
Hi Brian, The following three conditions must be satisfied for a VCF line to not be straight away
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Should haplotypes or primitive SNPs be used for RAiSD input?
Hi Brian, The following three conditions must be satisfied for a VCF line to not be straight away
6/3/20
Jaime Osorio
,
Nikolaos Alachiotis
5
8/16/19
Values on Omega report
Hi Nikos Now works !!! thanks for your help Jaime El mié., 14 de ago. de 2019 a la(s) 11:14, Nikolaos
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Values on Omega report
Hi Nikos Now works !!! thanks for your help Jaime El mié., 14 de ago. de 2019 a la(s) 11:14, Nikolaos
8/16/19
魏凯
,
Nikolaos Alachiotis
2
8/7/19
how to set up same detected regions between omegaplus and SweeD
Hi Kai, When you say that "the start position and end position is different", do you refer
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how to set up same detected regions between omegaplus and SweeD
Hi Kai, When you say that "the start position and end position is different", do you refer
8/7/19
K Kozak
,
pavlos
2
6/7/19
RAiSD and Sweed: edge effects and short scaffolds
Hi, Have you used the latest version of RAiSD? if not, to correct the problem for the small scaffolds
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RAiSD and Sweed: edge effects and short scaffolds
Hi, Have you used the latest version of RAiSD? if not, to correct the problem for the small scaffolds
6/7/19
Maj
, …
pavlos
6
4/12/19
How to calculate the P-values in OmegaPlus?
Dear Boris, this is not a very easy problem. I think that you should use one of the following
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How to calculate the P-values in OmegaPlus?
Dear Boris, this is not a very easy problem. I think that you should use one of the following
4/12/19
K Kozak
, …
pavlos
3
4/12/19
SweeD: choosing grid size with varied length scaffolds
Hi, it is not so important. You can follow any method you like. However, it is important for the
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SweeD: choosing grid size with varied length scaffolds
Hi, it is not so important. You can follow any method you like. However, it is important for the
4/12/19
weikai...@gmail.com
,
Nikolaos Alachiotis
9
3/29/19
What is the Position in SweeD and OmegaPlus report files ?
Yes it does. You need to include the -all command-line flag. On Fri, Mar 22, 2019 at 2:37 PM <
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What is the Position in SweeD and OmegaPlus report files ?
Yes it does. You need to include the -all command-line flag. On Fri, Mar 22, 2019 at 2:37 PM <
3/29/19
weikai...@gmail.com
,
Pavlos Pavlidis
2
12/14/18
OmegaPlus -seed
Hi Kai, Just put a random number there... whatever, eg 193834. It is needed just in case you have
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OmegaPlus -seed
Hi Kai, Just put a random number there... whatever, eg 193834. It is needed just in case you have
12/14/18
Rija Ratinahirana
11/22/18
Add Item to Glossary
Hi, is it possible to add items to the glossary, inside OmegaT+ and if so how to do it ? Thank you,
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Add Item to Glossary
Hi, is it possible to add items to the glossary, inside OmegaT+ and if so how to do it ? Thank you,
11/22/18
vineeth m r
,
Pavlos Pavlidis
3
10/16/18
Why the sweed output has the majority of the likelihoods as 0
Thank you Dr. Vineeth MR Ph.D Scholar Molecular Genetics Lab ICAR-NDRI Karnal, Haryana 132001 On Mon,
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Why the sweed output has the majority of the likelihoods as 0
Thank you Dr. Vineeth MR Ph.D Scholar Molecular Genetics Lab ICAR-NDRI Karnal, Haryana 132001 On Mon,
10/16/18
Halie Rando
,
Pavlos Pavlidis
3
10/15/18
OSFS file format (SweeD)
Dear Dr. Pavlidis, Thank you very much for your response. This information is very helpful. I do have
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OSFS file format (SweeD)
Dear Dr. Pavlidis, Thank you very much for your response. This information is very helpful. I do have
10/15/18
guanruo
,
Nikolaos Alachiotis
3
10/11/18
SweeD seems stucked with vcf 481 individuals and 6991 sites
Thanks for the reply. After 100 mins, SweeD successfully finished the analysis. 在 2018年10月11日星期四 UTC+
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SweeD seems stucked with vcf 481 individuals and 6991 sites
Thanks for the reply. After 100 mins, SweeD successfully finished the analysis. 在 2018年10月11日星期四 UTC+
10/11/18
duguyiw...@163.com
,
Nikolaos Alachiotis
6
10/11/18
postion from VCF
Here is an example: if you first SNP is at position 1 and your last is at position 1000, and you give
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postion from VCF
Here is an example: if you first SNP is at position 1 and your last is at position 1000, and you give
10/11/18
Rilquer Mascarenhas
,
Nikolaos Alachiotis
4
7/15/18
Using RADseq data assembled with reference genome: issue about distance between SNPs
Hi Rilquer, I fixed that in version 2.2.11. You can get the latest release here: https://github.com/
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Using RADseq data assembled with reference genome: issue about distance between SNPs
Hi Rilquer, I fixed that in version 2.2.11. You can get the latest release here: https://github.com/
7/15/18
Joe Colgan
,
Nikolaos Alachiotis
2
1/24/17
Using monomorphic sites as input in OmegaPlus
Hi Joe, There is no way to use monomorphic sites with OmegaPlus. OmegaPlus implements the omega
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Using monomorphic sites as input in OmegaPlus
Hi Joe, There is no way to use monomorphic sites with OmegaPlus. OmegaPlus implements the omega
1/24/17
Anna Page
,
Nikolaos Alachiotis
2
1/23/17
Grid size error
Hi Anna, The error you are getting is due to the fact that the grid size you chose is larger than the
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Grid size error
Hi Anna, The error you are getting is due to the fact that the grid size you chose is larger than the
1/23/17
Li Wang
,
Pavlos Pavlidis
3
11/9/16
omega plus does not work on macs simulated data
... I meant "since we developed SweeD"... sorry On Thu, Nov 10, 2016 at 1:02 AM, Pavlos
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omega plus does not work on macs simulated data
... I meant "since we developed SweeD"... sorry On Thu, Nov 10, 2016 at 1:02 AM, Pavlos
11/9/16
王丽
, …
Pavlos Pavlidis
5
9/28/16
omegaPlus input format
Dear Li, please correct me if I'm wrong: You have several reads that can be assembled into
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omegaPlus input format
Dear Li, please correct me if I'm wrong: You have several reads that can be assembled into
9/28/16