Bioinformatics Software available on the Human Genetics cluster
The following lists bioinformatics software available on calypso. The list below does not provide the actual commands that you would type to access the software. For usage details, visit the software documentation links provided (where available), or contact us for support. You may also want to try executing
ls /usr/local/bin/
on calypso to see the actual commands available.
- Absoft Fortran compiler
- APM - Affected Pedigree Member method of linkage analysis
- ARB - various tools for sequence database handling and data analysis
- Artemis - genome viewer and annotation tool
- Aspex - affected sib-pair exclusion mapping
- Autoscan - script for automation of MAKEPED/DOWNFREQ/PEDCHECK/ANALYZE
- Blade - Bayesian LinkAge DisEquilibrium mapping
- NCBI Blast
- BLAT - BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.
- ClustalW - Multiple sequence alignment
- CRI-MAP - construction of multilocus linkage maps
- Diseq - Likelihood-based linkage disequilibrium analysis
- EMBOSS - software for sequence analysis
- fasta - sequence comparison
- FastEH+ - model-free analysis and permutation test(s) of allelic association based on EH
- FBAT - family-based association tests
- FastSLINK - conditional simulation of genetic data on pedigrees
- Gassoc - test for linkage between multiallelic genetic markers and disease
- Genehunter - extraction of complete multipoint inheritance information from pedigrees
- GOLD - Graphical Overview of Linkage Disequilibrium
- Grace - WYSIWYG 2D plotting tool
- GRIND - analysis of systems of ordinary differential equations (ODEs) and maps
- Haploview - designed to simplify and expedite the process of haplotype analysis
- HapScope
- homoz - multipoint mapping of disease genes in nuclear pedigrees, including homozygosity mapping
- Intel Fortran compiler
- isPCR In-Silico PCR searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance.
- Java (Sun and IBM/Blackdown)
- LAMP - software for Linkage and Association Modeling in Pedigrees
- Lahey Fortran compiler
- LINKAGE - a series of programs for maximum likelihood calculation of LOD scores
- Loki - analysis of a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis
- Madeline - preparing, visualizing, and exploring human pedigree data used in genetic linkage studies.
- mapmaker/sibs - mapping of loci in nuclear pedigrees with two or more affected/phenotyped sibs
- mapmaker (exp/qtl)
- MDR
- Mega2 - data-handling program for facilitating genetic linkage and association analyses
- Mendel - exact statistical analysis of qualitative and quantitative traits
- Merlin - Multipoint Engine for Rapid Likelihood Inference
- Octave - high-level language, primarily intended for numerical computations
- OSA - Ordered Subset Analysis
- PBAT - Tools for the statistical analysis of family-based association studies
- PAP - Pedigree Analysis Package
- PDT - Pedigree Disequilibrium Test
- ped2spl - interfacing of and marker selection from standard LINKAGE input files to SPLINK and TRANSMIT
- Pedcheck - detection of marker typing incompatibilities in pedigree data
- Pedsys - tool for management of genetic, pedigree and demographic data
- PHASE: A program for reconstructing haplotypes from population data
- phrap/consed - DNA sequence assembler and finishing tools
- Prest - detection of pedigree errors by use of genome-screen data
- Pseudomarker - joint Linkage and LD analysis
- QTDT - family based tests of linkage disequilibrium
- QTL Cartographer - suite of programs to map quantitative traits using a map of molecular markers
- R - language and environment for statistical computing and graphics
- RHMAP - statistical package for radiation hybrid mapping
- SAGE - Statistical Analysis for Genetic Epidemiology
- Simped - simulation program to generate haplotype and genotype data for pedigree structures
- SimWalk2 - haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses
- Solar - genetic variance components analysis
- StepC - Statistical Explanation for Positional Cloning
- Superlink - exact genetic linkage analysis with input-output relationships
- Swig - allows a developer to wrap C/C++ functions for use with scripting languages
- TOPALi - detection of recombination in DNA sequence alignments
- Transmit - transmission disequilibrium testing
- Vitesse - Likelihood Calculation on Pedigrees
- WHAP - SNP haplotype analysis package