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arvestad / jprime

Probabilistic Inference of Molecular Evolution
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Cannot handle unrooted input trees #3

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Say tou want to use a starting tree that you have computed with e.g. fastphylo. 
If you use option -g to input the start tree, you will get an error message 
telling you that the input is not a binary tree. This is because unrooted trees 
typically have outdegree 3 at the "top". 

What is the expected output? What do you see instead?
Options:
1. To root the tree arbitrarily.
2. To find a root that minimizes the number of duplications.
3. To ignore the first trinary node and create two nodes that arbitrarily 
connect and roots the three subtrees.

Original issue reported on code.google.com by lars.arv...@gmail.com on 21 Aug 2013 at 8:52