[R] phylogenetic trees calculation

Federico Calboli f.calboli at ucl.ac.uk
Sun Aug 1 22:30:13 CEST 2004

Dear all,

I would like to ask you the following:

I have data about different manuscripts, together with data about the
presence/absence of copying errors, in the days when manuscript were
really manuscripts. I would ideally like to use the data to draw a
phylogenetic tree, so that I can infer which ms was copied from which.
The error presence/absence is coded in binary format. The plan is to use
a maximun parsimony tree approach. The data looks like this toy example:

        "ms1"   "ms2"   "ms3"   "ms4"
"err1"  0       1       0       0
"err2"  0       0       1       1
"err3"  1       1       0       0
"err4"  0       0       0       1
"err5"  1       1       1       0
"err6"  1       1       0       1
"err7"  0       1       0       0
"err8"  0       1       0       1

Additionally I have a vector of weights for the errors (and more info to
be possibly used). 

Does R have a set of fuctions of a library that will calculate the a
phylogenetic tree from such data? I installed "ape", but, despite
reading the docs, I cannot find a function that would calculate a tree
from data like mine (my sight may be getting worse though). Any
suggestion is welcome.


Federico Calboli

Federico C. F. Calboli

Dipartimento di Biologia Evoluzionistica Sperimentale
Università di Bologna
Via Selmi, 3
40126 Bologna - ITALY

Tel - +39 051 2094187
Fax - +39 051 2094286
f.calboli at ucl.ac.uk
fcalboli at alma.unibo.it

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