stamppPhylip: Export to Phylip Format
In StAMPP: Statistical Analysis of Mixed Ploidy Populations

Description Usage Arguments Details Author(s) References Examples

View source: R/stamppPhylip.R

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

1	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")