Biomedical Informatics Software

A large number of software packages are available to cancer center labs and BISR staff.

Licensed software on HICCC computers:

Application Company/Authors
Chromas Technelysium Pty Ltd
Feature Extraction Agilent
Flowjo -
Matlab MaTDworks
Mutation Surveyor Softgenetics
Application Source Description
GCG-Wisconsin Package Accelrys -
BRLMM Analysis Tool Affymetrix -
GeneChip Targeted Genotype Analysis Affymetrix -
GeneChip Genotype Analysis Affymetrix -
GeneChip Data Transfer Tools Affymetrix -
GeneChip System Affymetrix -
Gene Copy Number Analysis Affymetrix -
Expression Console Affymetrix -
Tiling Analysis Affymetrix -
Genscan Burge and Karlin -
FlinchTV GeoSpiza -
VectorNTI Invitrogen -
NIS-Element Nikon -
ABI 2500 Analyzer 1.41 and 2.01 ABI -
Application, Sequence Source Description
Molphy Adachi and Hasegawa  
Phred/Phrap/Consed Green et al.  
Rnabob Eddy  
Rnamot Eddy  
T-COFFEE Notredame A Multiple Sequence Alignment Package.
JavaTreeview Saldhana  
AAT Xiaogui Huang  
CustalX Higgins et al. multiple sequence alignment and phylogenetic tree building
ClustalW Higgins et al. multiple sequence alignment and phylogenetic tree building
Fasta Pearson  
BioPerl   Perl modules that provide many common bioinformatics tools for use in Perl scripts.
EMBOSS   a large package of sequence search and manipulation commands, similar to the GCG package
GCG Accelrys 200+ bioinformatics programs
HMMER Sean Eddy Programs for building HMMs.
Partek Partek MicroArray Package
Application, Phylogeny Source Description
PAML   "Phylogenetic Analysis by Maximum Likelihood". Built as 64-bit binaries on the SUN V880 with access to the full 32 GB of RAM.
Phylip Adachi and Hasegawa The Phylogeny Inference Package (C2B2 v. 3.5c)
Application, Microarray Source Description
The R Package   A language and environment for statistical computing and graphics.
Bioconductor   An open source and open development software project to provide tools for the analysis and comprehension of genomic data (bioinformatics)
BRBArrayTools NCI  
SAM Tibishirani et al.  
Cluster 3.0 Eisen and deHoon  
GenePattern MIT/Broad  
MEV TIGR Microarray package
PathwayGuide Draghici Microarray pathway analysis software
Application, Molecular Mechanics Source Description
X-PLOR   v. 3.851 - A System for X-ray Crystallography and NMR.