Command Lines in PAUP*

Using the Command Line Interface

1. Gettting Help
   1. At the command line interface, type a question mark (?) and press return
      1. paup> ?
      2. This will show you the commands that PAUP understands.
   2. Now select a command and view the options for that command:
      1. paup> hsearch ?
      2. This will show you the syntax for the keyword, followed by a list of available options.
      3. The options are shown in three columns
         1. Keyword
         2. Possible settings
         3. Current setting
   3. Remember that the general syntax for commands is
      1. keyword option1=setting option2=setting;
2. Use the command line interface to explore PAUP
   1. Suggestions:
      1. Using an alignment of your choice, compare the search speeds for heuristic searches using TBR, SPR, and NNI branch swapping
      2. Compare the results of heuristic searches using a simple addition sequence vs. random addition sequences.
      3. Compare the trees found with Parsimony, Maximum Likelihood, and Minimum Evolution
      4. Compare the trees found with Neighbor Joining and Minimum Evolution

Using a PAUP block to automate analyses

1. We have previously used PAUP blocks to automatically configure frequently used features of an analysis, such as automatically exluding suspect characters.
2. Entire analyses can also be automated with a PAUP block
   1. The syntax is the same as is used with the command line interface
   2. If you can figure out the sequence of commands that you would issue to run an analysis from the command line interface, you can put this same sequence of commands into a PAUP block and cause the analysis to run automatically
   3. Commands issued from the command line interface or PAUP blocks are often more convenient if you have an assumptions block with taxon sets, character sets, and other assumptions defined.
3. This is very useful!
   1. Complex analyses can be performed unattended
   2. Repetitive analyses can be performed with a minimum of human error
   3. Long runs can be restarted by a person unfamiliar with the analysis, and analyses can be precisely reproduced
4. Place the commands, in proper sequence, within a valid PAUP block (remember the NEXUS file format). Be sure to end each line with a semicolon, and remember that a logical line need not correspond with what is displayed on a single line.

Using PAUP on UNIX computers

1. Now that you know how to run PAUP from the command line interface, you are free of the Macintosh window interface!
   1. Paup is available for a wide variety of platforms, including some machines that are much faster and more stable than desktop machines.
   2. To execute PAUP on UMBI, log on (as PBIO699k) and type
      1. UNIXprompt> paup inputfile
      2. You will be confronted with the command line interface. Use it in the same way as you learned on the mac.
   3. PAUP blocks are particularly useful when using the command line interface
      1. You can edit the file with vi or any other unix editor, or you can edit it on a desktop computer and FTP the file to the UNIX computer.
2. Paup is also able to accept command-line redirection, so it is possible to store the data in one nexus file, and keep a standard series of PAUP commands additional files. The syntax for this is:
   1. UNIXprompt> paup datafile < commandfile
   2. It may take some experience to become comfortable with this approach, but it can be very powerful.

Pseudo-random number generators

1. If you automate analyses with any random component, it is very important that you provide a unique random number seed for each distinct random analysis
   1. True random number generators are rare
   2. Most programs use "pseudo-random number generators"
2. Pseudo-random number generators produce a sequence of numbers that seem to be random, and is in fact random for our purposes, but that follow a sequence that is predictable if you know the seed number that was used.
   1. It does not matter what seed number you use in PAUP (in phylip, the number must be odd), but it must be a different number for each run that you want to use a different random sequence
3. If you want to exactly repeat a random run, you can do it if you know the random number you used, so keep the random number recorded in your notes on your analyses.