Information on Scripts_real_data.zip and Scripts_simulated_data.zip:
Genelist_9sp_longtree_removed.txt: List of 8,595 gene titles. Needed to run the scripts for real data.
a48fubar.pl & c05fubar.pl: Run "HYPHYMP FUBAR.bf" on a linux environment. Paths must be modified to suit your system
a240deletion.pl & c07totaldeletion.pl: Detect deletions and non-excluded sites from a lineage pair (and using an outgroup).
a241deletionstack.pl & c08deletionlist.pl: Calculate weighted deletion rate from deletions detected from seven lineage pairs.
Note: in an earlier stage we used three different alignment methods, but we decided to only use PROBCONS in the final paper. If you need alignments for the other methods, or you need help in modifying these scripts to use on PROBCONS-only, please contact me at yzheng2@uni-koeln.de.