Hola!
We have some sequencing data, from amazonian fishes,
which only covers "dna basura", so no genes. The goal
is phylogenetic inference.
Is Bioconductor usefull for this, or are there other R
packages/ other software on the net?
Kjetil Halvorsen
Dear Kjetil,
I have done alot of phylogeny studies using
phylip that I interface with R using RSPython.
There is alos a package that is called phylogr
in R, but it doesn't do traditional phylogeny.
I would actually be interested in collaborating on
rewriting some of the phylogeny programs IN R.
Best
Susan Holmes
Statistics
Stanford
Dear Kjetil and Susan,
I am not sure about the functionalities but the "ape" program in CRAN
might do
some of what you want. With regards to PHYLOGR, no, it won't do
phylogenetic
inference ---it is targeted for the statistical analysis of data in a
phylogenetic context, but phylogenies are to be given to PHYLOGR.
Right now
PHYLOGR will not work on the latest R version because of a few silly
things
that I have not had time to fix yet (I am the maintainer).
For other programs, you might want to take a look at Joe Felsenstein's
list of
software
http://evolution.genetics.washington.edu/phylip/software.html
Best,
Ramón
On Friday 17 January 2003 02:10, Susan Holmes wrote:
> Dear Kjetil,
> I have done alot of phylogeny studies using
> phylip that I interface with R using RSPython.
> There is alos a package that is called phylogr
> in R, but it doesn't do traditional phylogeny.
> I would actually be interested in collaborating on
> rewriting some of the phylogeny programs IN R.
>
> Best
> Susan Holmes
> Statistics
> Stanford
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
******** Original query by K. Halvorsen **********************
On Friday 17 January 2003 00:57, kjetil brinchmann halvorsen wrote:
> Hola!
>
> We have some sequencing data, from amazonian fishes,
> which only covers "dna basura", so no genes. The goal
> is phylogenetic inference.
>
> Is Bioconductor usefull for this, or are there other R
> packages/ other software on the net?
>
> Kjetil Halvorsen
>
--
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
http://bioinfo.cnio.es/~rdiaz
APE might be the best. I've got some work mid-completion that has a
slightly different set of tools, but it isn't done yet.
>>>>> "susan" == Susan Holmes <susan@stat.stanford.edu> writes:
susan> Dear Kjetil,
susan> I have done alot of phylogeny studies using
susan> phylip that I interface with R using RSPython.
susan> There is alos a package that is called phylogr
susan> in R, but it doesn't do traditional phylogeny.
susan> I would actually be interested in collaborating on
susan> rewriting some of the phylogeny programs IN R.
susan> Best
susan> Susan Holmes
susan> Statistics
susan> Stanford
susan> _______________________________________________
susan> Bioconductor mailing list
susan> Bioconductor@stat.math.ethz.ch
susan> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
A.J. Rossini Rsrch. Asst. Prof. of
Biostatistics
U. of Washington Biostatistics rossini@u.washington.edu
FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org
-------------- http://software.biostat.washington.edu/
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Email
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