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User defined tree (Read 1926 times)
lun
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Curious HyPhy user

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User defined tree
Jan 16th, 2013 at 10:27pm
 
Dear Sergei,

If I submit an alignment to datamonkey with a user define ML tree. Should the tree be rooted with an outgroup first? Since the trees are quite different between rooted and unrooted trees.

Best regards,
lun
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Sergei
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Datamonkeys are forever...

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Re: User defined tree
Reply #1 - Jan 17th, 2013 at 8:55am
 
Hi Lun,

Rooted and unrooted versions of a tree MAY look different, but in fact they are essentially identical. Datamonkey will do a "mid-point" unrooting of the trees provided by users for computational efficiency. Most analyses (DEPS being the notable exception), will give you the same result regardless of how the tree is rooted, because they use time-reversible models. With DEPS, you can explicitly choose the outgroup to root on.

Sergei
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