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Converting rooted tree to unrooted

Converting rooted tree to unrooted - Bioinformatics

Converting rooted tree to unrooted - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 02-10-2011, 12:23 PM
Pipette Filler
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Default Converting rooted tree to unrooted



Hi,

I'm trying to come up with a phylogenetic tree for use with codeml. Codeml gives me a warning that my tree is rooted, and that an unrooted tree is required. How do I rewrite the following as an unrooted tree?

((scer,zrou),((klac,agos),(sklu,(kthe,kwal))));

Many thanks for your help,
Seán
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Old 05-18-2011, 07:53 PM
Pipette Filler
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Default Re: Converting rooted tree to unrooted

Remove the paranthesis around the second and third clade:

((scer,zrou),(klac,agos),(sklu,(kthe,kwal)));

Unrooted trees needs at least a trifurcation at the root (see the PAML FAQ).
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