| Program Name | Exons:Running the program at MUSC | Platform | Manuals | Home Page | Licensed? | Brief Description
| LOGO |
| CLUSTALW v1.7 | CLUSTALW
| UNIX | CLUSTALW-HTML
| None | Freeware
| Heuristic Multiple Alignment DNA/Protein-Molecular Evolution | | | | | | | |
| HMM v2.1.1 | HMM
| UNIX | HMM PDF,
HMM PS
| Sean Eddy's HMMER HOME | Freeware
| Position Specific Scoring Matrix is constructed from a Multiple Alignment via Hidden Markov Model
methods. HMMER Protein-Molecular Evolution
|  | | | | | | |
| MACAW | MACAW
| MAC OS & WIN95 | MACAW Documentation
| none | Freeware
| Multiple alignment-Molecular Evolution
|  | | | | | | |
| VISEUR | VISEUR
| UNIX, requires X-server software.
| VISEUR Documentation
| VISEUR Home | Freeware
| Makes TWO-D plots of membrane spanning proteins ( POSTSCRIPT output) ,tracks mutations,exports MSF files
and has an integral 3D viewer.
|  | | | | | | |
| ESPript v1.6 |
| UNIX | ESPript Index,
HELP
HELP2
| ESPript Home ESPript FTP site | Freeware
| Multiple alignment annotations
|  | | | | | | |
| SEQUOIA | SEQUOIA
| UNIX.
| Sequoia Documentation
| Sequoia Home | Freeware
| SEQUOIA is a computer program for the alignment of homologous protein sequences, and for the superpostion of homologous protein
atomic coordinates.
| | | | | | | |
http://www.lctn.u-nancy.fr/viseur/viseur.html
| Program Name | Exons:Running the program at MUSC | Platform | Manuals | Home Page | Licensed?
| Brief Description | LOGO |
| SYBYL-BASE,BioPolymer,CLogP/CMR,COMFA,CSCORE, Advanced COMFA,COMPOSER,CONCORD, DISCO, DYANA, Dynamics,FlexiDock, FUGUE, HINT,LEAPFROG,
Legion/CombiLibMaker,MATCHMAKER, MARDI_GRAS, MOLCAD,MOLCONNZ, MOPAC, MM3, NMR-TRIAD, PROTABLE, QSAR, SELECTOR, SITEID, UNITY,
UNITY3D, VolSurf, ZAP, ZINDO
| SYBYL
| UNIX based but available via x-server software from MAC OS & WIN95 | All documents are on-line. Start SYBYL and look under HELP menu. | TRIPOS | Licensed and Paid For
| Molecular Modeling, NMR, Drug Discovery 3D database searching
|  | | | | | | |
| RASMOL | RASMOL
| MAC OS & WIN95 | TEXT | RASMOL | Freeware
| Nifty Molecular Viewer
|  | | | | | | |
| NANOVISION | NANOVISION
| MAC OS | Hardcopy Checkout Only | None | Licensed and paid for
| Nifty Molecular Viewer
| 
| | | | | | |
| MACSPARTAN | MACSPARTAN
| MAC OS | Hardcopy Check Out | MACSPARTAN | Licensed and Paid For.
| Nifty Molecular Viewer with some Calculations capacity; can deal with animations
|  | | | | | | |
| SPARTAN | SPARTAN
| UNIX-PHOTON Only 2 Users | Hardcopy Check Out | SPARTAN | Licensed and Paid For.
| The mothership for MACSPARTAN. Ab initio, semi-empirical and molecular mechanics.
| | | | | | | |
| AMBER6 | AMBER6
| UNIX-only | Here are the AMBER ver. 6.0 manuals as PDF files
| AMBER | Licensed and Paid For.
| Assited Model Building with Energy Refinement
|  | | | | | | |
| GROMOS 96 | GROMOS 96
| UNIX-only | Hardcopy Check Out ONLY | GROMOS | Licensed and Paid For.
| Biomolecular Simulation.
|  | | | | | | |
| GAUSSIAN98 | GAUSSIAN 98
| UNIX-only | Hardcopy Check Out ONLY and Technical Info On-line from GAUSSIAN | GAUSSIAN98 | Licensed and Paid For.
| Biomolecular Simulation of the ab initio sort.
|  | | | | | | |
| LOOK/GeneMine v3.5 | Look/GeneMine
| UNIX-only | Help and Tutorials are On-line | GeneMine/Look Home | Licensed and Paid For.
| Automated Sequence analysis and management plus Homology Modeling.
|  | | | | | | |
| SwissPDBViewer 3.5b1-Win95,3.1 MAC | SwissPDBViwer
| MAC OS & WIN95 | TEXT | SwissPDBViwer Manual | Freeware
| Viewing,rendering Alignment & Homology Modeling
|  | | | | | | |
| HYPERCHEM Version 4.5 | HYPERCHEM
| WIN95 Only | Hardcopy Check Out | HyperChem | Licensed and Paid For.
| Nifty Molecular Viewer with some Calculations capacity; can deal with animations
|  | | | | | | |
| Alchemy 2000 | Alchemy 2000
| WIN95 Only | Hardcopy Check Out | ALCHEMY | Licensed and Paid For.
| Nifty Molecular Viewer with some Calculations capacity; can deal with animations
|  | | | | | | |
| Babel 1.1 | Babel 1.1
| UNIX Only ( Erg2 and Janus Only ) | Babel Readme | Babel | Shareware.
| Molecular file format interconversion program; PDB or MOL2 to VRML.Input formats.
and Output formats.
|  | | | | | | |
| PDB2VRML | PDB2VRML
| UNIX Only | PDB2VRML manual
| PDB2VRML Home
| Shareware.
| Molecular file format interconversion program; PDB or MOL2 to VRML.
|  | | | | | | |
| MAESTRO 3.0 | MAESTRO
| UNIX Only | Hardcopy and On-line via GUI | MAESTRO
| Licenced One User at a time.
| GUI for Molecular modeling programs JAGUAR, and MACROMODEL.
|  | | | | | | |
| JAGUAR 4.1 | JAGUAR
| UNIX: Only available on
lobo.musc.edu | Hardcopy and On-line via GUI | JAGUAR
| Licenced One User at a time.
| Very fast, pseudospectral based ab initio Molecular Modeling package.
|  | | | | | | |
| Macromodel 7.1 | Macromodel
| UNIX Only | Hardcopy and On-line via GUI and linked below
| Macromodel
| Licenced One User at a time.
| Molecular mechanics modeling program.
|  | | | | | | |
| MOPAC2000 | MOPAC2000
| UNIX Only | Hardcopy and On-line via GUI | MOPAC2000
| Licenced One User at a time.
| Semiempirical Molecular Orbital calculations for large systems.
|  | | | | | | |
| MODELLER4/ MODELLER6v0 | MODELLER4,
MODELLER6v0
| UNIX Only | Modeller4 Manual,
Modeller6v0 Manual |
Modeller7v0
| Licenced .
| HOMOLOGY modeling by satisfaction of spatial constraints.
|  | | | | | | |
| GRASP 1.3.6 | GRASP
| UNIX Only | GRASP Manual
(This is a long document and its slow to load. Be Patient!) |
GRASP
| .
| GRASP (Graphical Representation and Analysis of Structural Properties)is a molecular visualization and
analysis program. GRASP is particularly useful for the display and manipulation of the surfaces of molecules and
their electrostatic properties.
|  | | | | | | |
| DELPHI | DELPHI
| UNIX Only | DELPHI Manual
(This is a long document and its slow to load. Be Patient!) |
DELPHI
| .
| A program to solve the PB equation in 3D, using non-linear form, incorporating
2 dielectric regions, ionic strength, periodic and focussing boundary conditions,
utilizing stripped optimum successive over-relaxation and an improved algorithm
for mapping the Mol. Surface to the finite-Difference grid.
|  | | | | | | |
| Program Name | Exons:Running the program at MUSC | Platform | Manuals | Home Page | Licensed? | Brief Description
| LOGO |
| MAKEPED | Makeped
| UNIX only | Nothing on-line
| Linkage Home | Licensed.
| Converts a preliminary datafile containing pedigree data into a format suitable for use by the
preplink program.
|  | | | | | | |
| PREPLINK | PREPLINK
| UNIX only | None On-line.
| Linkage Home | Licensed.
| Accepts output files from makeped and formats files for use by FASTLINK, and GENEHUNTER.
| | | | | | | |
| FASTLINK (unknown,ilink,mlink,lodscore,linkmap ) | FASTLINK
| UNIX only | None On-line
| Linkage Home | Licensed.
| Evaluates linkage data contained in properly formatted datafiles.
| | | | | | | |
| LCP,LSP and LRP | Linkage Auxilliary
Programs
| UNIX only | None On-line
| Linkage Home | Licensed.
| Evaluates linkage data contained in properly formatted datafiles.
| | | | | | | |
| GENEHUNTER - Complete Linkage Analysis (version 2.0 beta (r2)) | GeneHunter
| UNIX only | Nothing on-line.
| LINKAGE Home | Licensed.
| Evaluates linkage data contained in properly formatted datafiles.
| | | | | | | |
| Jurg Ott's Homogeneity Programs:HOMOG (homog,homog1a,homog1b,homog2,homog3,homog3r homog4,point4,mtest)
| HOMOG
| UNIX only | HOMOG Manual HOMOG
| HOMOG | Licensed.
| From the manual: Homog carries out a homogeniety test (A-test) under the following alternative
hypothesis: two family types, one with linkage between a trait (or any gene locus forthat matter)
to a marker or map of markers, the other without linkage.
| | | | | | | |
| SOLAR (Sequential Oligogenic Linkage Analysis Routines)
| SOLAR
| UNIX only | SOLAR Manual SOLAR
| SOLAR | Licensed.
| From the manual: SOLAR carries out genetic variance component analyses including linkage analysis,
quatntitative genetic analysis and covariate screening.
|  | | | | | | |
| Sanger Centre Image 3.9, | Image 3.9
| UNIX only | IMAGE Help Manual IMAGE3.9
| Sanger Image Home | Licensed.
| IMAGE 3.9 provides an image processing system for fingerprint gel experiments and fully supports the FPC program.
|  | | | | | | |
| Sanger Centre FPC v-4.6.4, | FPC
| UNIX only | FPC Help Manual
FPC postscript, FAQ
| Sanger FPC Home | Licensed.
| Evaluates fingerprint Gel data. Can be used to examine the Human BAC Fingerprint database
| | | | | | | |
| QTDT - Quantitative TDT 2.1.11 | QTDT
| UNIX only | QTDT Help Manual
QTDT
| QTDT Home | Licensed.
| Performs quantitative transmission disequilibrium tests to evaluate linkage in the presence
of
linkage disequilibium.
| | | | | | | |
