Help with Phylip

James O. McInerney jamm at nhm.ac.uk
Tue Mar 10 12:10:12 EST 1998


Tom,

You are almost there.

When you draw a neighbor-joining tree you will, naturally get branch lengths. 
This is because the tree is derived from a set of distances and the algorithm
will use these distances in order to specify branch lengths.

After bootstrapping, the program CONSENSE is also producing a tree, but this
tree is not derived from distances, it is derived from 100 other trees.  The
consensus tree is a cartoon, depicting a tree that is most compatible which
those partitions that were seen most often.  So, the final consensus tree has
nothing to do with branch lengths, it is simply a depiction (a graphical
representation, if you will) of the majority-rule consensus of the 100
bootstrapped trees.

A very popular approach is to take the original NJ tree and to place the
bootstrap support values on the internal nodes of the tree and also to put the
branch lengths (from the original, unbootstrapped data) on the internal branches.

Of course, a poorly-supported internal partition might appear in the original
NJ tree, but will not find its way into the final bootstrapped consensus tree,
so you will have to look up the bootstrap partition table to find out how much
support it received.


Hope this is not too confusing.

James


Tom Fagan wrote:
> 
> I was wondering if any kind soul out there could help me with a dilemma.
> I have used the software in the Phylip package to generate some phylogeny
> data, using in the following order, Seqboot (100replicates), protdist,
> neighbor, consense.  The trouble is that the output from consense doesn,t
> give any branch lengths and when I draw the tree with TreeView although
> the scale bar appears it is obviously meaningless.  Now the output from
> neighbor does have distances but 100  of them, it seems that in making a
> consensus tree this data does not get carried over, yet I have seen
> publications where the same applications were used and the nice little
> scale bar appears on the tree.  How is this scale calculated? Am I doing
> something wrong, - anyone got any ideas,
> 
> thanks,

-- 
=========
James O. McInerney               email: J.mcinerney at nhm.ac.uk
Molec. Biol. Comput. Officer,    phone: +44 171 938 9247
Department of Zoology,           Fax:   +44 171 938 9158
The Natural History Museum,
Cromwell Road,                    
London SW7 5BD.                  
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