Batch files

Batch files are ways to give PAUP commands without going through the menus (Mac) or entering items one at a time in the command line (all platforms). For example, you could set up a PAUP batch file which would do a heuristic search saving the best trees from each addition sequence replicate, save these trees to a file, filter for the best trees, and finally save these best trees to a second tree file. Batch files are also a good way to ensure consistency between searches — for example. you won't have to remember if you used 5 or 10 addition sequence replicates per bootstrap replicate, as that information will be in the batch file. A batch file has the following format:

#nexus [Tells PAUP that this is a NEXUS file]
begin PAUP; [Starts the PAUP block]
[PAUP commands]; [Gives PAUP instructions on what to do — the same thing you enter in the command line]
end; [Ends the PAUP block]

To create a batch file, first create a new document within PAUP or in some other text editor (such as SimpleText). Then type "#nexus" in the first line and "begin paup;" in the second. After that, include the PAUP commands you want — PAUP's command reference document, available from the downloads section of its website, is invaluable in constructing these. Finally, write "end;" at the end of the document. Save the document. Now, executing the document, the same way you execute a data file, will start the commands running.

All the batch files on this website can be copied into a new PAUP document and executed. Several of the batch files have places to insert the name of a file or set, often appearing as [name]. Make sure that the brackets are removed: for example, if the file is called tree1, "file=[name]" should become "file=tree1". PAUP makes batch file troubleshooting easy — if there is a problem with the file, PAUP will open the file and put the cursor where the error occured. PAUP does not see anything in brackets, so comments written there will not affect analyses. The only two exceptions to this are:

1. Iif the first character within the bracket is an exclamation point, PAUP will display the contents in the display buffer; and
2. Trees can have a [&U] or [&R] to tell PAUP if they are rooted or not.