stamppPhylip {StAMPP}

Export to Phylip Format

Description

Converts the genetic distance matrix generated with stamppNeisD into Phylip format and exports it as a text file

Usage

stamppPhylip(distance.mat, 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

Author(s)

Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>

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)
# Export the genetic distance matrix in Phylip format
## Not run: stamppPhylip(potato.D.pop, file="potato_distance.txt")