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

NEXUS

[ Trees from file: argj.distances ]

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

:2.71,'argj_neime':0.41):41.21):3.77,((('argj_arcfu':30.43,
'argj_metth':29.00):2.04,'argj_aqui':45.30):4.05,(('argj_rhofa'
:21.29,'argj_strcl':27.10):24.48,('argj_deira':30.89,'argj_theth'
:25.20):5.60):8.36):0.63):3.10,'argj_bacst':28.59):0.25,
(((argjsyny:18.78,'argj_synys':11.53):11.63,(argjarad:15.15,'argj_arath'
:20.37):27.93):7.19,((((argjyeas:15.76,'argj_yea':15.41):14.36,
argjschpo:26.81):14.94,((argjarful:21.14,(argjmtth:17.73,argjmetja
:16.80):3.83):5.93,argjbacsu:29.03):5.29):7.44,(argjlacto
:11.28,'argj_lacpl':11.00):25.34):4.13):9.85):14.84,('argj_thema'
:4.77,'argj_thene':5.02):14.84):0.00;
endblock;
>



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