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lliu1871 / phybase

Phybase provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees
GNU General Public License v3.0
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How to do the correlation analyses between simulated genetrees and empirical gene trees? #2

Open Galaxy-228 opened 2 years ago

Galaxy-228 commented 2 years ago

Hi, liang: After done the simulation of gene trees using Phybase, i want do a correlation analyses between simulated genetrees and empirical gene trees , like this: 图片 Thanks so much !! How to do this analysis ? Thanks so much !!

lliu1871 commented 2 years ago

It seems that you only need to simulate gene tree topologies. I suggest that you reestimate branch lengths of the astral tree using MP-EST. Then use the function sim.coal.mpest in Phybase to simulate gene trees.

Liang

Liang Liu Graduate Coordinator Department of Statistics Institute of Bioinformatics University of Georgia Phylogenetics Lab | Phylogenetics Lab (uga.edu)http://faculty.franklin.uga.edu/lliu/ @.***

From: Jie @.> Sent: Tuesday, July 19, 2022 6:13 AM To: @.> Cc: @.***> Subject: [lliu1871/phybase] How to do the correlation analyses between simulated genetrees and empirical gene trees? (Issue #2)

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Hi, liang: After done the simulation of gene trees using Phybase, i want do a correlation analyses between simulated genetrees and empirical gene trees , like this: [??]https://user-images.githubusercontent.com/53716512/179726241-5d77376a-dcd0-4742-bf92-901addc225d7.png Thanks so much !! How to do this analysis ? Thanks so much !!

— Reply to this email directly, view it on GitHubhttps://github.com/lliu1871/phybase/issues/2, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACZITQUTMVCYCWZETTOYGMTVUZ5TTANCNFSM537NAMVQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Galaxy-228 commented 2 years ago

Hi,Liang: Thanks for your reply and suggestions! I want simulate gene trees under different value of Theta, then is it feasible to just use the function sim.coal.mpest ?

lliu1871 commented 2 years ago

Then you need theta and a species tree with branch lengths in mutation units in order to simulate gene trees.

Liang

Liang Liu Graduate Coordinator Department of Statistics Institute of Bioinformatics University of Georgia Phylogenetics Lab | Phylogenetics Lab (uga.edu)http://faculty.franklin.uga.edu/lliu/ @.***

From: Jie @.> Sent: Wednesday, July 20, 2022 3:50 AM To: @.> Cc: Liang @.>; @.> Subject: Re: [lliu1871/phybase] How to do the correlation analyses between simulated genetrees and empirical gene trees? (Issue #2)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi,Liang: Thanks for your reply and suggestions! I want simulate gene trees under different value of Theta, then is it feasible to just use the function sim.coal.mpest ?

— Reply to this email directly, view it on GitHubhttps://github.com/lliu1871/phybase/issues/2#issuecomment-1189945716, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACZITQQTMKKRIMHBCKOCKY3VU6VUDANCNFSM537NAMVQ. You are receiving this because you commented.Message ID: @.***>

Galaxy-228 commented 2 years ago

Thanks so much !! Best wishes~