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repmaker (for MOAB)


Repmaker is a program by Jim Wilgenbusch designed to "parallelize" the phylogenetic non-parametric bootstrap analysis. Repmaker automatically generates multiple NEXUS files. The files are then used to distribute a single PAUP* bootstrap analysis over multiple machines by using the MOAB or MAUI job manager.  If you are using another job schedule like Condor see the Repmaker for condor page.  


  • PAUP. Edit the repmaker perl file and specify the name and path for your paup binary.
  • A NEXUS command file named "input.nex" in the current working directory. The input.nex file contains a paup block with all the paup commands that will be executed for each bootstrap replicate. The file might have a paup block with model parameters and the names of sequences to be deleted. For example:
begin paup;
delete 1;
set crit=likelihood;
lset nst=2 tratio=4.71 rates=gamma shape=0.4036;


Running repmaker

$ repmaker <filename>
Repmaker takes a single optional argument; the name of a NEXUS data file. If a file name is not given, then the program will query you for one once it is started. Also, the program will be ask you to input the total number of bootstrap replicates to be included in your analysis and how many times you would like to divide up the total number of replicates.

When the program finishes you will find a directory named RepFiles. The RepFiles directory contains the individual bootstrap replicate files, a condor command file, and a perl script for putting things back together after all replicates finish.

After running repmaker

repmaker with condor

Change to the RepFiles directory automatically generated by the repmaker program

$ cd RepFiles

Run the submitAll command

$ submitAll

Consolidate the results

After all the reps finish, return to the RepFiles directory and execute the perl script named

$ ./

The script will concatenate all of the individual bootstrap tree files and get paup to save the consensus treefile to repMakerBS.tre.

If you want to transfer things to your Mac or PC so that you can print a pretty picture, you will need to move the following files:

  • allReps.out
  • getTrees.nex
  • YourDataFile.nex

The getTrees.nex file will have to be changed to reflect the location of your data file on your Mac or PC. The getTrees.nex file will look something like this:

begin paup;
execute ~/anolis/anolis_crist.nex; [<---- !!!! CHANGE THIS LINE !!!!!]
gettrees allblocks=yes StoreTreeWts=yes file=allReps.out mode=3;
contree all/strict=no majrule=yes usetreewts=yes treefile = repMakerBS.tre;

Change the execute line as noted.