[Molecular-evolution] Phylip

Joe Felsenstein joe at removethispart.gs.washington.edu
Sun Sep 10 08:34:52 EST 2006


In article <mailman.787.1156872367.20007.mol-evol at net.bio.net>,
percy  <hopercyhp at gmail.com> wrote:
>
> can't get the scale bar from treeview after seqboot (1000replicates),
>prodist, neighbor, consense. As you said because after bootstrapping, the
>program consense is not derived from distances. The final consensus tree has
>nothing to do with branch lengths. 
>
>So, what can I do? Do you have any suggestion?

Read the main documentation file of PHYLIP, the Frequently Asked Questions
section.  There, the 8th question (and answer) is:

 Consense gives wierd branch lengths! How do I get more reasonable ones?"
    Consense gives branch lengths which are simply the numbers of replicates 
  that support the branch. This is not a good reflection of how long those 
  branches are estimated to be. The best way to put better branch lengths on a 
  consensus tree is to use it as a User Tree in a program that will estimate 
  branch lengths for it, such as DnaML. You may need to convert it to being an 
  unrooted tree, using Retree, first. If the original program you were using 
  was a program that does not estimate branch lengths, you may instead have to 
  use one that does. You can use a likelihood program, or make some distances 
  between your species (using, for example, DNADIST) and use FITCH to put 
  branch lengths on the user tree. Here is the sequence of steps you should go 
  through:

       1. Take the tree and use Retree to make sure it is Unrooted (just read 
  it into Retree and then save it, specifying Unrooted)
       2. Use the unrooted tree as a User Tree (option U) in one of our 
  programs (such as FITCH or DNAML). If you use FITCH, you also first need to 
  use one of the distance programs such as DNADIST to compute a set of 
  distances to serve as its input.
       3. Specify that the branch lengths of the tree are not to be used but 
  should be re-estimated. This is actually the default. 

This problem comes about because the Consense consensus tree program does
not go back to the original data, but uses the individual trees from the
bootstrap replicates.  You will find a discussion in the Consense documentation
file of the issue of putting branch lengths on consensus trees, and why it is
difficult.

----
Joe Felsenstein         joe at removethispart.gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 357730, Seattle, WA 98195-7730 USA



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