PHYLIP

Sean Turner turner at ncbi.nlm.nih.gov
Thu Mar 15 04:04:30 EST 2001


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>> As I understand, the values then produced at the nodes in the Consense 
>> Outfile are the values that you need to put in the tree for publication 
>> purposes for examples. These values, do you place them at the nodes or along 
>> the branch lengths? 
>
>As you want. Personaly I favor the first solution. However, when I want to 
>compare MP and NJ, I like to put one value above the branch and one under. 
>
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In my opinion, it is inappropriate to put support values at the nodes of
unrooted trees; rather, they should be placed on the branches.  For
example, consider the following unrooted tree with 100% support for the
central branch:

((fungus,fish),(chimp,human))

While the partition of (fungus,fish) from (chimp,human) receives 100%
support, this is not to say that the ancestral node connecting fungus
and fish receives 1007 support.  Fish are not more closely related to
fungi than they are to primates.  One might say that it is the node
connecting chimp and human that receives 100% support, but this implies
knowledge of the root of the tree; i.e., it is no longer unrooted.  In
such a case, if one were to subsequently root the tree like so:

(fungus,(fish,(chimp,human)))

then I think it safe to say that the node for (chimp,human) can be said
to receive 100% support.


Sean Turner, Ph.D.
NCBI (GenBank)
National Library of Medicine
NIH, Building 45, Room 6AN.12        phone: 301-435-8943
45 Center Drive, MSC 6510            fax: 301-480-2918
Bethesda, MD 20892-6510, USA         e-mail: turner at ncbi.nlm.nih.gov

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