ASRs?

[vinjlynch]

Hi All,

In the past I have used the "classic" datamonkey website to do ancestral state reconstructions, but it is no longer an option and the new website doesn't have an ASR option. Is there a tutorial on how to do ASRs in HyPhy 2.5.18?

Thanks Vinny

[spond]

Dear @vinjlynch,

Take a look at https://github.com/veg/hyphy-analyses/tree/master/AncestralSequences

Many analyses (e.g BUSTED, aBSREL) have the option to save a fit file, which you can then feed to the ancestral sequence tool. Let me know if that works for you. Do you want to reconstruct all sequences or estimate a particular one?

Best, Sergei

[vinjlynch]

Will give it a try, is there an option for protein alignments? We’re not interested in all ASRs but a subset > 1.

Best, Vinny

Vincent J. Lynch, Ph.D. Assistant Professor Department of Biological Sciences University at Buffalo, SUNY 551 Cooke Hall Buffalo NY, 14260

vjlynch@buffalo.edumailto:vjlynch@buffalo.edu

“... the most useful thing we can do is to repudiate, and so we repudiate” – I. Turgenev, Fathers and Sons (1862)

"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, On The Origin of Species (1859)

On Oct 1, 2020, at 1:35 PM, Sergei Pond notifications@github.com<mailto:notifications@github.com> wrote:

Dear @vinjlynchhttps://github.com/vinjlynch,

Take a look at https://github.com/veg/hyphy-analyses/tree/master/AncestralSequences

Many analyses (e.g BUSTED, aBSREL) have the option to save a fit file, which you can then feed to the ancestral sequence tool. Let me know if that works for you. Do you want to reconstruct all sequences or estimate a particular one?

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/veg/hyphy/issues/1228#issuecomment-702288934, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANAFRRGXKKKJLMGEHGE2VB3SIS4VNANCNFSM4SAWVOWQ.

[spond]

Dear @vinjlynch,

What does your workflow look like? I can point you to the right analysis settings.

Best, Sergei

[vinjlynch]

We actually haven’t established one yet, other than working on AA alignments so suggestions would be welcome.

Best, Vinny

Vincent J. Lynch, Ph.D. Assistant Professor Department of Biological Sciences University at Buffalo, SUNY 551 Cooke Hall Buffalo NY, 14260

vjlynch@buffalo.edumailto:vjlynch@buffalo.edu

“... the most useful thing we can do is to repudiate, and so we repudiate” – I. Turgenev, Fathers and Sons (1862)

"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, On The Origin of Species (1859)

On Oct 1, 2020, at 4:16 PM, Sergei Pond notifications@github.com<mailto:notifications@github.com> wrote:

Dear @vinjlynchhttps://github.com/vinjlynch,

What does your workflow look like? I can point you to the right analysis settings.

Best, Sergei

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/veg/hyphy/issues/1228#issuecomment-702373284, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANAFRRAZJC36SMK2ZZ62XC3SITPRXANCNFSM4SAWVOWQ.

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