The original programs in the suite were originally written by Vamsee Reddy, many have been updated and new programs have been added by different members of the lab and collaborators.

Find below the list of programs available. Scripts developed by our group as dependencies are not listed here but are included in the distribution:

1. protocol1.py (Manual)
2. protocol2.py (Manual)
3. gsat.py (Manual)
4. gblast3.py (Manual)
5. tmstats.py (Manual)
6. tss.py (Manual)
7. ssearch.py (Manual)
8. ancient.py (Manual)
9. quod.py (Manual)
10. hvordan.py (Manual)
11. tmsplit.py (Manual)

• Note 1:
  The BioV manual needs to be updated.

• Note 2:
  Some improvements to protocol 2 and other programs were introduced by Gabriel Moreno-Hagelsieb.

• Note 3:
  Pranav Iddamsetty and Arturo Medrano added the scripts tmsplit.py and tmsFunction.py. These programs provide a command-line interface to cut transporter sequences under the same criteria as the website:
  http://biotools.tcdb.org/bartms_split.html

• Note 4:
  The program gblast3.py was improved by Pranav Iddamsetty Gabriel Moreno-Hagelsieb and Arturo Medrano.

• Note 5:
  The programs quod.py, tcblast.py and hvordan.py were added by Kevin Hendargo and Arturo Medrano. The script quod.py runs WHAT from the command line on one or more sequences and is able to generate the plots in different formats and qualities. The script tcblast.py provides functions to run blast against tcdb from the command line and provides graphical display that will be used by the last script hvordan.py, which runs blast and WHAT in order to generated an html ouput file that will help the user to make the biological interpretation of protocol2 top hits.