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Bioinformatics Software available at OSC

Amber- a molecular simulation program

bioperl - offers a set of perl modules which can be used for sequence manipulation

BLAT - a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments

CERF* - Collaborative Electronic Research Framework (CERF) is a network storage system that offers workgroup collaboration, access control, version control, and digital signatures in a multi-user setting.

ClustalW - a general purpose multiple sequence alignment program for DNA or proteins

EMBOSS - a sequence analysis package specially developed for the needs of the molecular biology user community

ExtractProp* - a portable application for extracting properties from computational biology applications

Galaxy - a program for dynamic transitive closure analysis

HMMER - profile HMMs for protein sequence analysis

Mascot Search Engine - a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases.

Mitoprot - a software program permitting the study and prediction of mitochondrion-related proteins

MrBayes - a program for the Bayesian estimation of phylogeny

Multicoil - a program for predicting two- and three-stranded coiled-coils

NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

NCBI Toolkit - a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information

Ohio BioSciences Library* - a suite of high-performance bioinformatics applications designed for use on large memory SMP and cluster computing systems alike

Partek Pro* - Partek Pro is an integrated, scalable software environment capable of analysis and transformation of millions of records or millions of variables

PCBL (Portable Cray Bioinformatics Library) - a portable implementation of the Cray Bioinformatics Library interface.

Phylip - a package of programs for inferring phylogenies

Predotar - a program for predicting sequence properties

Stata - a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics

TimeLogic DeCypher - a suite of applications for accelerating intensive bioinformatics algorithms

* Indicates software available through OSC's Statewide Software License Distribution

Availability by machine

Name
Altix
BALE
Cluster
Itanium-2
Cluster
Intel P4
Cluster
Opteron
Cluster
AMBER
No
bioperl
No
No
No
No
BLAT
No
No
No
No
CERF*
Available through OSC's Statewide Software License Distribution
ClustalW
No
No
No
No
EMBOSS
No
No
No
No
ExtractProp*
Available for download
Galaxy
No
No
No
No
HMMER
No
No
No
No
Mascot Search Engine
Available at OSC-Springfield
Mitoprot
No
No
No
No
MrBayes
No
No
No
No
Multicoil
No
No
No
No
NAMD
No
No
NCBI
No
No
Ohio BioSciences Library*
Available through OSC's Statewide Software License Distribution
Partek Pro*
Available through OSC's Statewide Software License Distribution
PCBL
No
No
Phylip
No
No
No
No
Predotar
No
No
No
No
Stata
No
No
No
TimeLogic DeCypher
No
No
No
No