INPUT FILES

PHRAPL requires two input files: an assignment file (e.g. cladeAssignments.txt) and a file with phylogenetic trees in newik format (e.g. trees.tre). All files must have the same taxon names (labels) across all loci.

You can have missing data. PHRAPL does not require gene trees to include all individuals/alleles per population/species/group.

You can include both haploid and diploid data in the same analyses using the argument popScaling in the GridSearch function.

Table of contents

• Assignment File
• Gene Trees