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How to do the correlation analyses between simulated genetrees and empirical gene trees? #2
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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/>
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From: Jie ***@***.***>
Sent: Tuesday, July 19, 2022 6:13 AM
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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 !!
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Hi,Liang: |
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
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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 ?
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Thanks so much !! |
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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:
Thanks so much !!
How to do this analysis ?
Thanks so much !!
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