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rooted trees and assymetrical models (Read 1573 times)
wayne
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rooted trees and assymetrical models
May 16th, 2008 at 8:07am  
Hi Sergei, quick ?. is ACCEPT_ROOTED_TREES only a necessity for optimizing a non-reversible model, and not for simulating under one. as I understand it the simulation process is by default rooted? thanks ./w
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Sergei
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Re: rooted trees and assymetrical models
Reply #1 - May 16th, 2008 at 9:04am  
Dear Wayne,

Everything is necessarily rooted (for computational definitiveness), but if you don't set ACCEPT_ROOTED_TREES, HyPhy may

1). Reroot the tree for computational speedups
2). Collapse a bifurcating root node to have three children

HTH,
Sergei
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