Introduction to PAUP*

PAUP* (pronounced "pawp-star") is a flexible program for phylogenetic analysis that is capable of a wide range of analytical techniques. We will start by using PAUP as a program for parsimony analysis, and in later weeks will explore some of it other capabilities.

• PAUP* was generously provided for our use by its author, Dave Swofford (Smithsonian LMS), in a test version. You should be aware when you use this test version that there are some restrictions on its use:
  • You may not copy the program or give it away. If you want to use it outside of the context of this class, you should arrange to become an official tester.
  • You may not publish the results of analyses without explicit permission from Swofford. This permission is usually automatically granted, and the restriction is primarily for your own protection. Remember that this is a test version of the software. It is possible that some bugs still remain.
  • If you detect any bugs in the program, you are obliged to:
    • Work to determine if the bug can be made reproducible
    • Report the bug to Dave Swofford (typically you will first report the bug to me [Delwiche]).

 

The Nexus File Format

1. MacClade and PAUP* both use the "nexus" file format, so the file can be opened in PAUP simply by dragging the file icon to the PAUP* icon.
2. The nexus file format
   1. The file begins with the string #NEXUS
   2. All information is organized in blocks
      1. Some blocks are used by more than one program
      2. Any block that a program does not understand will be ignored.
   3. Each block is composed of a series of lines
      1. Each line begins with a command (keyword), followed by arguments that modify the command
      2. Each line ends with a semicolon
      3. A logical line may span more than one line as displayed in the editor.
   4. The structure of blocks
      1. Each block begins with a line with the keyword "begin" followed by the name of the block, and ends with a line "endblock" (or "end").
      2. Within each block are lines that contain information that will be used by the program.

   #NEXUS
   Begin Taxa;
   Dimensions NTax=4;
   TaxLabels fish frog snake mouse;
   End;
   Begin Characters;
   Dimensions NChar=20;
   Format DataType=DNA;
   Matrix
   	Fish	ACATA GAGGG TACCT CTAGG
   	Frog	ACTTA GAGGC TACCT CTACG
   	Snake	ACTCA CTGGG TACCT TTGCG
   	Mouse	ACTCA GACGG TACCT TTGCG
   ;
   End;
   Begin Trees;
   Tree best=(fish, (frog, (snake,mouse)));
   End;
   

• Find the beginning and end of the three blocks.
• Where does the line that begins with "Matrix" end? Hint: look for the next semicolon.
• Notice the notation that is used to store the tree.

Phylogeny from the Bottle Exercise

1. Mount the server Flora
2. Open the structural character set that you developed last week in PAUP*
3. Familiarize yourself with the PAUP* layout
   1. At the bottom of the windows menu you should find the name of the file you just opened. If you select this file, PAUP will open a data editor window and display the file.
   2. Notice that PAUP* displays the text of the file rather than displaying a specialized character editor as does MacClade. Some types of files are easier to edit in MacClade, but editing sequence files, I prefer to use the PAUP* editor.

Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. Nexus: an extensible file format for systematic information. Syst. Biol. 46:590-621.