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.
- 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
Warning: this page is large.
- A Documentation System for C/C++ and Java. Used JavaDoc-like
- 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