search

rbouckaert / snapper

7 stars 3 forks source link

Can we use snapper to estimate divergence time? #2

Open xiekunwhy opened 3 years ago

xiekunwhy commented 3 years ago

Hi,

Can we use snapper to estimate divergence time using snps like SNAPP?

Best, Kun

rbouckaert commented 3 years ago

Hi Kun,

In principle, snapper can do the same as SNAPP, but faster. It will provide relative divergence times just like SNAPP does.

Cheers, Remco

xiekunwhy commented 3 years ago

Hi Remco,

Thank you for your answers.

And I think many users want to known how to get absolute divergence time using snapper. Would you please provide a tutorial to tell us how to get absolute divergence time using snapper? Like https://github.com/mmatschiner/tutorials/blob/master/divergence_time_estimation_with_snp_data/README.md

Best, Kun

rbouckaert commented 3 years ago

Hi Kun,

Thanks for the suggestion. I passed on your request to David Bryant, who maintains the package.

Cheers,

Remco

davidjamesbryant commented 3 years ago

Thanks Kun. I'll look into adapting Michaels excellent tutorial. It should be a matter of a single edit (although with SNAPPER you would not reduce the number of samples per population).

-David.

xiekunwhy commented 3 years ago

Hi David,

Glad to hear that. And hope SNAPPER tutorial coming soon.

Best, Kun

xiekunwhy commented 3 years ago

Hi @davidjamesbryant ,

Any progress?

Best, Kun

davidjamesbryant commented 3 years ago

No, too much teaching at the moment.

David

======================= Prof David Bryant Dept Mathematics and Statistics University of Otago Aotearoa New Zealand

On 13/04/2021, at 7:49 PM, xiekunwhy @.***> wrote:



Hi @davidjamesbryanthttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdavidjamesbryant&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C4b1e33bfecaf41190e7808d8fe509933%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637538969486391177%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iMGvr4XdTtQIJtcAdBUNddOYgvbs37ztncF5i2VSHKg%3D&reserved=0 ,

Any progress?

Best, Kun

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frbouckaert%2Fsnapper%2Fissues%2F2%23issuecomment-818523550&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C4b1e33bfecaf41190e7808d8fe509933%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637538969486401134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wVEvWvTnD3Mb9i0bdq88s%2Fgpw5pUbWdYsi1PDAfltFM%3D&reserved=0, or unsubscribehttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAATIGSFOAEXPOGFMGU3MUT3TIPZORANCNFSM4ZFWZZRA&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C4b1e33bfecaf41190e7808d8fe509933%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637538969486401134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=i0NQSCHXoMBEyFb0wuRtKvvWEDhvLF5cTNR2VzALKT0%3D&reserved=0.

xiekunwhy commented 3 years ago

Hi David,

So sorry to trouble you, I will just keep waiting.

Best, kun

MarnusStoltz commented 3 years ago

Dear Kun,

There is now a tutorial for SNAPPER available, link below:

https://github.com/ForBioPhylogenomics/tutorials/tree/main/divergence_time_estimation_with_snp_data

Note that this is for running SNAPPER from a cluster. It does however include a script to generate your Beast xml files for SNAPPER (for more general use).

Also, a more general tutorial is coming soon.

Regards Marnus

davidjamesbryant commented 3 years ago

BAFFF!!!!!

======================= Prof David Bryant Dept Mathematics and Statistics University of Otago Aotearoa New Zealand

On 28/06/2021, at 9:18 PM, Marnus_Stoltz @.***> wrote:



Dear Kun,

There is now a tutorial for SNAPPER available, link below:

https://github.com/ForBioPhylogenomics/tutorials/tree/main/divergence_time_estimation_with_snp_datahttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FForBioPhylogenomics%2Ftutorials%2Ftree%2Fmain%2Fdivergence_time_estimation_with_snp_data&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C32ed02da23c54332b99f08d93a15ac35%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637604687038479116%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=H1Yher5t5anLon3UiR1GhM4qLSB2CIPyzEUvB2wu5eY%3D&reserved=0

Note that this is for running SNAPPER from a cluster. It does however include a script to generate your Beast xml files for SNAPPER (for more general use).

Also, a more general tutorial is coming soon.

Regards Marnus

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frbouckaert%2Fsnapper%2Fissues%2F2%23issuecomment-869520232&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C32ed02da23c54332b99f08d93a15ac35%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637604687038479116%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=P3su5SrxyARQ2slODzCCdZ7yyMO6Xe432Ig2iRHSMxs%3D&reserved=0, or unsubscribehttps://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAATIGSD2TFWPMVPFKVWA7UTTVA45VANCNFSM4ZFWZZRA&data=04%7C01%7Cdavid.bryant%40otago.ac.nz%7C32ed02da23c54332b99f08d93a15ac35%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637604687038489060%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RKgjNyG4WZ4tflpOpYVkw7Yj6GiQpp3sMJyfZ2EWE7k%3D&reserved=0.