OmegaPlus

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Brian Arnold, … Peter Civáň7

Jun 28

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

Jun 28

demetris taliadoros, Nikolaos Alachiotis6

Mar 22

RaisD and the sfs_code2ms converter

Hello Nikos, Thanks again. A quick solution I found now is to convert the SFS_CODE output to fasta

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RaisD and the sfs_code2ms converter

Hello Nikos, Thanks again. A quick solution I found now is to convert the SFS_CODE output to fasta

Mar 22

Alexander Klassmann, … Jordan Bemmels7

10/21/20

SweeD does not report correct CLR for folded spectra

Hi again, An update: I tested out the tentative solution I mentioned on several empirical datasets

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SweeD does not report correct CLR for folded spectra

Hi again, An update: I tested out the tentative solution I mentioned on several empirical datasets

10/21/20

Karine Durand, N.Alachiotis2

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.Alachiotis2

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.Alachiotis2

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

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.Alachiotis6

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 Alachiotis11

6/4/20

SweeD error - number of nucleotides

So, I checked the vcf file with vcf-validator and found that there was a line that did not have the

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SweeD error - number of nucleotides

So, I checked the vcf file with vcf-validator and found that there was a line that did not have the

6/4/20

Brian Mack, Nikolaos Alachiotis2

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 Alachiotis5

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 Alachiotis2

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, pavlos2

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, … pavlos6

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, … pavlos3

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 Alachiotis9

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 Pavlidis2

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 Pavlidis3

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 Pavlidis3

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 Alachiotis3

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 Alachiotis6

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 Alachiotis4

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 Alachiotis2

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 Alachiotis2

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 Pavlidis3

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 Pavlidis5

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

lwgbi...@gmail.com, N.Alachiotis2

9/22/16

input and result about combine Sweed and omega

Hi, On Friday, August 26, 2016 at 5:28:24 AM UTC+3, lwgbi...@gmail.com wrote: dear all： i am useing

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input and result about combine Sweed and omega

Hi, On Friday, August 26, 2016 at 5:28:24 AM UTC+3, lwgbi...@gmail.com wrote: dear all： i am useing

9/22/16

Yafei Mao, Pavlos Pavlidis7

7/30/16

How to use CLR value & p-value to figure out outlier ?

Hi Pavlos, Thanks a lot. I will try my best. Best, Yafei 2016-07-28 16:53 GMT+09:00 Pavlos Pavlidis

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How to use CLR value & p-value to figure out outlier ?

Hi Pavlos, Thanks a lot. I will try my best. Best, Yafei 2016-07-28 16:53 GMT+09:00 Pavlos Pavlidis

7/30/16

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