RELAX more than 1 FG

[VinnyLynch]

Hi All,

Is there a way to have more than 1 foreground lineage in RELAX. For example, we have a a phylogeny of a gene family with functional genes (outgroup), pseudogenes (ingroup), and re-functionalized pseudogenes (deeply nested within the ingroup). We'd like to test if there is relaxation of selection on the pseudogenes and intensification on the re-functionalized pseudogenes using the ancestral functional genes as the background.

Best, Vinny

[spond]

Dear @VinnyLynch,

There exists a version of RELAX that allows you to define N groups of lineages and then test whether or not there is relaxation on any of them as a group. It other words, you fit N-1 relaxation coefficients (one per group that is not the background), and ask if any of them are different from 1. Is that something you are interested in?

Best, Sergei

[VinnyLynch]

Hi Sergei,

Thanks, that version of RELAX sounds like exactly what I'm looking for!

Vinny

Sent from my iPhone

On Aug 14, 2017, at 7:24 AM, Sergei Pond notifications@github.com<mailto:notifications@github.com> wrote:

Dear @VinnyLynchhttps://github.com/vinnylynch,

There exists a version of RELAX that allows you to define N groups of lineages and then test whether or not there is relaxation on any of them as a group. It other words, you fit N-1 relaxation coefficients (one per group that is not the background), and ask if any of them are different from 1. Is that something you are interested in?

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/veg/hyphy/issues/589#issuecomment-322176350, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK4YXtAF6wIshZSsOrsrTNFH6fs-WRkeks5sYDx8gaJpZM4OyWEj.

[spond]

Dear @VinnyLynch,

OK, let me dig it up and confirm which version of HyPhy it works with. I'll post the code and the instructions shortly.

Best, Sergei

[VinnyLynch]

Thanks!

Sent from my iPhone

On Aug 14, 2017, at 8:22 AM, Sergei Pond notifications@github.com<mailto:notifications@github.com> wrote:

Dear @VinnyLynchhttps://github.com/vinnylynch,

OK, let me dig it up and confirm which version of HyPhy it works with. I'll post the code and the instructions shortly.

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/veg/hyphy/issues/589#issuecomment-322188393, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK4YXlHPotVnjx3HoeFUJiqF-SeKEbVwks5sYEoagaJpZM4OyWEj.

[spond]

Dear @VinnyLynch,

v2.3-dev branch includes a file TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf It adds synonymous rate vacation and multi-class testing.

Let me know if this works for you.

Best, Sergei

[VinnyLynch]

Hi Sergei,

Thanks for the info. Does RELAX-SRV.bf require HyPhy v2.3 or can it be run under the old v2.2 GUI?

Best, Vinny

[spond]

Dear @VinnyLynch,

v2.3

Best, Sergei

[VinnyLynch]

Thanks!

Vincent J. Lynch, Ph.D. Assistant Professor Department of Human Genetics Department of Organismal Biology & Anatomy The University of Chicago 920 E. 58th Street | CLSC 325B | Chicago, IL 60637

Office: 773-834-1326 Fax: 773-834-8470 vjlynch@uchicago.edumailto:vjlynch@chicago.edu

"There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859

On Aug 25, 2017, at 12:12 PM, Sergei Pond notifications@github.com<mailto:notifications@github.com> wrote:

Dear @VinnyLynchhttps://github.com/vinnylynch,

v2.3

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/veg/hyphy/issues/589#issuecomment-324981993, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK4YXgNZU3EONHZVEEXY8WHRSyGGA2jIks5sbwCVgaJpZM4OyWEj.