EditAttachPrintable
r50 - 16 Oct 2007 - 17:27:04 - SteveThompsonYou are here: TWiki >  TechHelp Web > ScSBioinformatics

SCS Bioinformatics Services

Application Resources

Bioinformatics resources presently exist on three systems at SCS. General use Linux computers should all mount a /usr/common/ directory structure that contains many bioinformatics tools. Plus, those Mac OS X computers that mount /usr/common have access to roughly the same suite of tools. Launch the program with the name of the tool in the chart below in most cases. Read the online documentation to find individual program names to use in those cases where the tool is a package containing multiple programs.

Furthermore, the FSU High Performance Computing (HPC) cluster has most of the same resources plus the commercial Accelrys Wisconsin Genetics Computer Group (GCG) sequence analysis software package, and the public domain EMBOSS sequence analysis software suite. The old GCG Mendel server has been retired by SCS.

platform account tool function documentation comment
SCS Linux and OS X computers SCS user ID or personal login sequence analysis and phylogenetics
clustalw multiple sequence alignment ClustalWHelp  
clustalx graphical user interface for clustalw ClustalXHelp requires X11 for display
muscle multiple protein sequence alignment User Guide  
mummer genome alignment package Manual 19 different scripts, launch each by name
mauve genome alignment system User Guide mauveAligner (command line) and mauve.GUI (requires X11)
readseq sequence format converter ReadSeqHelp readseq.GUI (requires X11) also available
paup phylogeny inference package Command Reference Dr. David Swofford
mb MrBayes - Bayesian inference of phylogenies Manual Dr. Fredrik Ronquist
phylip phylogeny inference package Documentation 35 different programs, launch each by name
phyml maximum likelihood phylogeny inference interactive menu help, command-line help  
puzzle Tree-Puzzle - maximum likelihood phylogeny inference by quartet puzzling Manual  
paml maximum likelihood analysis of sequence data and phylogenies User's Guide 8 different programs, launch each by name, get control file here
modeltest likelihood model decision tree Documentation get modelblock file here
tv TreeView - phylogenetic tree display and plot Manual requires X11 for display
migrate-n estimation of migration rate and effective population size Documentation Dr. Peter Beerli
lamarc Likelihood Analysis with Metropolis Algorithm using Random Coalescence Documentation  
molecular visualization and manipulation
rasmol open source version of Roger Sayles molecular viewer Manual requires X11 for display
spdbv Deep View Swiss-PDB Viewer User Guide requires X11 for display
Cn3D NCBI molecular viewer for ASN.1 structure data Tutorial requires X11 for display
HPC dedicated HPC account use the HPC Web form to request an account
FSU's HPC has most of the above software plus:
the Accelrys Wisconsin Package (Genetics Computer Group v.11): gcg comprehensive sequence analysis package Manual over 150 different command line programs
seqlab GCG graphical user interface built-in help requires X11 for display
EMBOSS European Molecular Biology Open Software Suite Documentation over 160 different command line programs

Help

ssh login required for remote terminal access to all SCS machines. ssh X tunnelling required to display X11 windows on remote terminals (Note 1: the X MUST be capitalized for this option to work!). Like this:

ssh -X user@host.scs.fsu.edu

Where "user" is your login ID and "host" is the name of the SCS computer.

(Note 2: try ssh -Y [capital -Y 'trusted' X11 tunnelling] if you encounter X11 display errors, especially with Mac OS X)

Refer to my Basic command-line UNIX tutorial for general assistance with the UNIX command line and other operating system issues.

See Alex Stuy's excellent Help page for assistance with ssh and X11 on Microsoft Windows systems.

See each program/package's individual Help documentation in the table above for specific "how to" questions.

Contact me at stevet@bio.fsu.edu for personal assistance.

Workshops

We have a MiniWorkshop series on using phylogenetic inference software at the UNIX command-line that we've developed for the Biology Ecology and Evolution Group.

Also see my GCG workshop series for an effective way to learn SeqLab and the Wisconsin Package.

Last changed: 16 Oct 2007 Steve Thompson

Edit | Attach | Printable | Raw View | Backlinks: Web, All Webs | History: r50 < r49 < r48 < r47 < r46 | More topic actions
 
SCS TWiki

This site is powered by the TWiki collaboration platformCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding TWiki? Send feedback