A MiniWorkshop on Using Phylogenetic Software at the UNIX command line

A three part 'mini-workshop' series on using phylogenetic inference software at the UNIX command line developed by the Computational Evolutionary Biology Group (CEB) at the Florida State University School of Computational Science (SCS).

*Three consectutive Thursday sessions October 6, 13, and 20, 2005, from 9:30 to 11:00 AM, in Dirac 152.*

Many biologists are familiar with the phylogenetic inference software PAUP* in the Macintosh 'Classic' GUI (Graphical User Interface) environment. However, running PAUP* in GUI mode on a personal Mac computer is not incredibly efficient, as any other running applications dramatically slow down its progress.

Learning and using the UNIX command line with a server-based PAUP* application can take the load off your personal computer, to free it up for more important things, like that latest manuscript you're trying to write. Furthermore, other phylogenetic inference software, such as MrBayes, only run through a command line interface. Moreover, the UNIX server environment is inherently more stable than your desktop environment - this helps keep your multiple day analyses running for as long as it takes. Getting access to these resources requires network access to UNIX server computers, and the ability to comfortably operate in the UNIX command line environment.

Instructors:

• Steve Thompson
• David Swofford
• Jim Wilgenbusch
• Johan Nylander

Sessions

Part One: Getting comfortable at the UNIX command line

Instructor - Steve Thompson

Key Points

• Connecting: ssh
• The UNIX Operating System and the Shell
• Editing files: vi, emacs, pico, and desktop applications
• Transferring files: scp and sftp (Fugu and other GUIs)
• the UNIX 'background' - batch processing

Related resources

• Command-line Basics: http://bio.fsu.edu/~stevet/ComputingBasics.pdf

Part Two: the PAUP* command line

Instructor - David Swofford

Key Points

• Understand the NEXUS file format
• Learn to run analyses from the command-line
• Learn shortcuts and tips to using PAUP*
• What to do when problems arise

Related resources

• PAUP* web site: http://paup.csit.fsu.edu
• Quick Start Tutorial: http://paup.csit.fsu.edu/Quick_start_v1.pdf
• Command Reference: http://paup.csit.fsu.edu/Cmd_ref_v2.pdf
• NEXUS sample datasets: http://paup.csit.fsu.edu/nfiles.html

Part Three: more PAUP* & MrBayes, CONDOR

Instructors - Jim Wilgenbusch and Johan Nylander

Key Points

• review previous session information
  • unix commands
  • screen sessions
  • NEXUS files
  • submitting PAUP* jobs in batch mode
• introduction to MrBayes
• introduction to Condor submission

Related resources

• MrBayes manual (PDF)
• Sample NEXUS data file for MrBayes (text)
• MrBayes lab instructions (PDF)
• AWTY -- a tool for examing convergence
• MrAIC.pl -- a tool for model selection
• SCS computer resources
• Using Condor at SCS
• Using Condor to run PAUP
• Using condor to run MrBayes
• Running the bootstrap analysis in parallel using repmaker

User Comments

Last changed: 29 Aug 2007