Computational Biology Documentation at UC Santa Cruz

Linear HMM Software
The SAM system for sequenace alignment and modeling---one of our workhorse programs. Documentation for locally-installed version
Dirichlet mixtures
Dirichlet mixtures used in various projects for modeling the prior expectation of the distribution of amino acids.
A2M multiple-alignment format
Most of the SAM tools use the A2M format for multiple alignments, as it is one of the few formats that can express unaligned positions.
CVS Version Control
How to use our local version of CVS.
Simple, flat-file relational databases. Download the RDB 2.6c source: This copy is patched to correctly handle sorting numbers in exponential form. Requires PERL5 and GNU sort (gsort).
Support vector machine software
Unix commands for accessing the bioinfomatics database at GenomeNet
Gnuplot Version 3.6 beta
Installed as the command gnuplot3.6. Warning: this page is large.
A Documentation System for C/C++ and Java. Used JavaDoc-like syntax.
Get the path to a DSSP file, downloading if necessary.
Get the path to a HSSP file, downloading if necessary.
Get the path to a PDB file, downloading if necessary.
PDB Info Files
Abbreviated PDB file and ATOM/SEQRES alignment in RDB format.
Get the path to a PDB info file, create if necessary.
UCSC Internal Documentation Directory

Baskin Center for Computer Engineering and Information Sciences
University of California, Santa Cruz
Santa Cruz, CA 95064