Overview of the Perl scripts in this directory
----------------------------------------------

This directory contains a collection of (mostly horrible)
Perl scripts. Some of them are still maintained, such as 
phylo_pl.pl. 

Some of the scripts in this directory relay heavily
on forester.pm.



RIO pipeline:
- rio.pl
- makeTree.pl
- p7extract.pl
- multifetch.pl


Running a parallelized RIO web server:
- nph-riowebserver
- rio_slave.pl
- rio_slave_driver.pl
- queue.pm


To prepare data to be used by RIO:
- bootstrap_cz.pl
- pfam2slx.pl
- extractSWISS-PROT.pl
- extractTrembl.pl
- pfam2pwd.pl


To run multiple RIO analyses in an automated fashion:
- Xrio.pl


To analyze RIO results (of Xrio.pl runs):
- bootstrapCounter.pl
- bootstrapSelector.pl
- diffFinder3.pl


Counting of species in SWISS-PROT and TrEMBL:
- countSpeciesSPTrEMBL.pl