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Patristic distances

Mike Syvanen syvanen at ucdavis.edu
Fri Aug 4 17:28:28 EST 2000

Vijay Aswani wrote:

> Hi,
> I am trying to produce patristic distance matrices, hopefully from PAUP or
> phylip tree files with branch lengths. PAUP* lets you produce such a matrix
> but only parsimony as a criterion.
> So far, the only program I could find to do this is TREDIS which runs in DOS
> and has been crashing a lot. Does anyone know of any programs to do this? I
> would be willing to write something myself, if someone would help me with
> the logic of how to extract pairwise distances from the tree file.
> Alternatively, can anyone suggest some pseudocode I could use to write a
> program to do this?
> Thanks,
> Vijay

The following is the output for a distance tree that is in a
nexus file format. This was computed using a nearest-neighbor
alogorthm in the package of programs provided by GCG; I
believe this format is used by many of the programs that
are out there.  The numbers adjacent to each
taxa and clade give branch lengths and it is a straightforward matter to
add them to get patristic distances.  This is preferrable to using patristic
distances in PAUP.

Mike Syvanen


[ Trees from file: argj.distances ]

begin trees;
utree Tree_1 = (((((('argj_corgl':26.29,'argj_myctu':21.54):29.73,('argj_neigo2'



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