all_hds.phy - alignment used for the paralog and branch length analysis

all_hds.nj.tre - neighbor-joining tree generated with default parameters in Phylip used in paralog and branch length analysis

count_species_specific_clades.pl - script used to parse all_hds.nj.tre to identify species-specific clades.

calculate_average_root_tip.pl - script used to parse the output of TreeStat and calculate the average branch lengths (see Methods).

