Converts the genetic distance matrix generated with stamppNeisD into Phylip format and exports it as a text file
Arguments
- 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
Details
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
References
Perrier X, Jacquemound-Collet JP (2006) DARWin - Dissimilarity Analysis and Representation for Windows. Agricultural Research for Development
Examples
# 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, "standard")
# Export the genetic distance matrix in Phylip format
if (FALSE) stamppPhylip(potato.D.pop, file="potato_distance.txt")