Here is a collection of software tools and databases developed by different groups at UC Davis. Those tools are provided as is. You use it as your own risk. The contact information if any in software codes or documentations can be used to contact the author, but there is no guarantee to response.
Genome Center Bioinformatics Core, Dawei Lin's group
Scripts from David Neale's group
Scripts from Ian Korf's group
Tools and Applications from Oliver Fiehn's group
Tools from J. Clark Lagarias's group
Homolmapper is a free, open-source application for mapping homology information from a protein sequence alignment onto a structure file, allowing one to examine homology in a structural context. Homolmapper is a command-line Python application written in the Lagarias lab at UC Davis. It is available under a license from The Regents found at the Download instructions. The structure must be in PDB format. The output is a new PDB file which can be readily examined in the structure-viewing program of one’s choice (the author of homolmapper prefers VMD).
A generic Blast script running job on a cluster by Prof. Yong Duan
c shell script click here