Vijay Aswani wrote:
>> 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?
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.
[ Trees from file: argj.distances ]
utree Tree_1 = (((((('argj_corgl':26.29,'argj_myctu':21.54):29.73,('argj_neigo2'