Patristic distances

Korbinian Strimmer korbinian.strimmer at zoology.oxford.ac.uk
Tue Aug 8 12:49:39 EST 2000


On 4 Aug 2000, Vijay Aswani wrote:

> I am trying to produce patristic distance matrices, hopefully from PAUP
> or phylip tree files with branch lengths.


You can do this in Java using PAL (http://www.pal-project.org).
PAL contains a class called TreeDistanceMatrix which does what you want:

  http://users.ox.ac.uk/~strimmer/pal/api/pal/tree/TreeDistanceMatrix.html

To use this class you will have to program in Java.  If you don't want
to do that you could simply use the SHOWTREE program from the Vanilla
package

  http://users.ox.ac.uk/~strimmer/vanilla/

As PAL and Vanilla is written in Java it should run wherever you
want it to run.


> Alternatively, can anyone suggest some pseudocode I could use to write a
> program to do this?

Fast o(n^2) pseudo-code for this is in  D.Bryant and P. Wadell. 1998. MBE
15:1346-1359


Best regards,

  Korbinian



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