Export to Phylip Format
Converts the genetic distance matrix generated with stamppNeisD into Phylip format and exports it as a text file
stamppPhylip(distance.mat, file = "")
distance.mat |
the matrix containing the genetic distances generated from stamppNeisD to be converted into Phylip format |
file |
the file path and name to save the Phylip format matrix as |
The exported Phylip formated text file can be easily imported into sofware packages such as DARWin (Perrier & Jacquemound-Collet 2006) to be used to generate neighbour joining trees
Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
Perrier X, Jacquemound-Collet JP (2006) DARWin - Dissimilarity Analysis and Representation for Windows. Agricultural Research for Development
# import genotype data and convert to allele frequecies data(potato.mini, package="StAMPP") potato.freq <- stamppConvert(potato.mini, "r") # Calculate genetic distance between populations potato.D.pop <- stamppNeisD(potato.freq, TRUE) # Export the genetic distance matrix in Phylip format ## Not run: stamppPhylip(potato.D.pop, file="potato_distance.txt")
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.