[R-sig-phylo] Read in Splitstree network in R

2014-11-04 Thread Benjamin Ward (ENV) 
Hi,

I have a need to collect from some networks I've generated in Splitstree, the 
patriotic distances between each pair of taxa, and also the number of splits or 
otherwise the amount of loop or web structure in the network. I figured if I 
can read the .nex files generated by SplitsTree into an R session with one or 
more of the Phylo packages I could easily extract this information, make a 
table and do some plots. I've only used APE for tree manipulation with R so 
far. What do I need to read in networks?

Thanks,
Ben.



[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Re: [R-sig-phylo] Read in Splitstree network in R

2014-11-04 Thread Simon Joly 
Dear Ben,

You will find scripts that will help you perform some of the tasks you want
to do (read SplitsTree nexus files, calculate network patristic distances)
in the supplementary material that comes with this paper:

Volkmann L., Martyn I., Moulton V., Spillner A., Mooers A.O. 2014.
Prioritizing Populations for Conservation Using Phylogenetic Networks. PLoS
ONE. 9:e88945.

It should be a good start...

Best wishes,
Simon


2014-11-04 6:58 GMT-05:00 Benjamin Ward (ENV) b.w...@uea.ac.uk:

 Hi,

 I have a need to collect from some networks I've generated in Splitstree,
 the patriotic distances between each pair of taxa, and also the number of
 splits or otherwise the amount of loop or web structure in the network. I
 figured if I can read the .nex files generated by SplitsTree into an R
 session with one or more of the Phylo packages I could easily extract this
 information, make a table and do some plots. I've only used APE for tree
 manipulation with R so far. What do I need to read in networks?

 Thanks,
 Ben.



 [[alternative HTML version deleted]]

 ___
 R-sig-phylo mailing list - R-sig-phylo@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
 Searchable archive at
 http://www.mail-archive.com/r-sig-phylo@r-project.org/


[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/