Kyle McNamara
This is a collection of all the source code used to control the work flow for all the prediction, alignment, and tree drawing software used in this project.
- masterHandle.py
- handleSeqTree.py
- splitPDB.py
- runsplitPDB.py
- pullSeqFromPDB.py
- runClustal.sh
- kmutils.py
- makeChainFile.py
- getStuctures.py
These scripts all accept a list of filenames for the .pdb files of structures to be analyzed. And, for output they generate a comma-separated distance matrix to be passed along to the tree drawing program.
- runClick.py
- runDeepAlign.py
- runFatCat.py
- Fatcat.sh
- runMatt.py
- runTMAlign.py
- neighborjoin.sh
- printunrooted.py
- index.html
- analysis.html
- input.php
- result.php
- about.html
- contact.html
- override.css
This is a list of all the installed software being used for this project.
- DeepAlign (structure alignment)
- FATCAT (structure alignment)
- Click (structure alignment)
- Modeller (for use by Click)
- Matt (structure alignment)
- TMalign (structure alignment)
- ClustalW (sequence alignment)
- PHYLIP (tree construction)
- Mechanize (Python - tree printing)
- Bootstrap (webpage)
Updated 6/14/13