Datatypes in Brownie

[flugcanje]

Hello all,

I am currently running Brownie 2.1.2 on a Linux computer running Ubuntu.

Is there any way I can feed nucleotide alignment data to Brownie? or at least a way in which the data could be reinterpreted so that it's readable by Brownie?

I want to do an RRT between two monophyletic clades, I have 52 taxa and now one gene with about 950 positions.

Thanks for any help,
carlos


Also a comment on installation, in case someone needs it:

I kept trying to compile it with the make command but it would give me an error stating that the file fstream.h did not exist.
After looking around a bit I found a way to fix it:

On every .cpp file on the main brownie-src folder, the lines that say:

#include <fstream.h>
#include <iomanip.h>

must be changed to:

#include <fstream>
#include <iomanip>

So, just delete the .h and everything should work golden!

Cheerio

Carlos J. Rivera-Rivera
University of Geneva
Department of Genetics and Evolution

[Brian O'Meara]

You could convert it to discrete data and treat it that way. However, the model it would use would basically be JC (unless you modified the discrete transition matrix). For this sort of question, you might look at other software, like PAML.

Best,

Brian

_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info

Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara

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