Open xiekunwhy opened 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
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
Hi Kun,
Thanks for the suggestion. I passed on your request to David Bryant, who maintains the package.
Cheers,
Remco
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.
Hi David,
Glad to hear that. And hope SNAPPER tutorial coming soon.
Best, Kun
Hi @davidjamesbryant ,
Any progress?
Best, Kun
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:
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.
Hi David,
So sorry to trouble you, I will just keep waiting.
Best, kun
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
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.
Hi,
Can we use snapper to estimate divergence time using snps like SNAPP?
Best, Kun