Finding Maximum Likelihood Bootstrap Phylogeny Trees with PAUP and lavaRepMaker

Runs multiple maximum-likelihood bootstrap phylogeny tree searches across the Dell-Platform LSF cluster (which does not use Condor) and then collates the results, finding a majority-rules consensus tree. Contact Mike Wong for copies of lavaRepMaker.

Synopsis

Here is an example use of lavaRepMaker

UNIX Shell Command

    lavaRepMaker SPWA_cytbMLbtstp.unix -treps 80 -notify always -email "mikewong@sfsu.edu"

Usage

This section describes, in general, what kinds of options are available to lavaRepMaker. You can get this information by typing lavaRepMaker, without options, at the command prompt.

UNIX Shell Command

[mikewong @ccls ~]$ lavaRepMaker
Usage:

   lavaRepMaker <Nexus file> [lavaRepMaker options]

lavaRepMaker options (see PAUP command reference for details)

    -treps n
        The number of bootstrap replicates

    -nodes n
        The number of nodes available for processing. Default is 40.

    -notify (error|completion|never|always)
        Conditions to notify the user via e-mail. Default is never.

    -email
        E-mail address used to notify the user.

    -search
        Heuristic or Branch-and-Bound search options.

Notification conditions

• error notifies the users of errors upon failure of the job to complete normally
• completion notifies the user when the job is complete (or fails) and where the log files are for results and errors.
• never will not e-mail the user about any of the maximum likelihood bootstrap searches; however, if an e-mail address is supplied, the user will receive an e-mail when the consensus tree is completed.
• always notifies the user when the job begins processing, when the job is completed (or fails) and when the consensus tree is completed.

Generated Files

lavaRepMaker generates quite a few files while running; this section briefly explains what each file stores

   logs/
     error.<job id>.log Errors for each job
     results.<job id>.log Status and outcome for each job
   jobs/
     rep-node<node id>.nex PAUP commands for each job
   <Nexus file>.<node id>.tre The maximum-likelihood tree for a given job
   getTrees.pl A script which performs the collation and starts the majority-rules consensus
   getTrees.nex PAUP commands to find the majority-rules consensus

Output File

The output file is stored in the current working director as:

  consensus.tre -- The majority-rules consensus tree results

Optional input file

lavaRepMaker can accept an input file in order to refine the parameters for phylogenetic analysis after the original input file has been processed by paup (but before the ML bootstrap trees have been generated).

input.nex -- A file which specifies additional behavior for the ML bootstrap

Sample input.nex

input.nex should be in the same directory as the genome data. lavaRepMaker will look for this file in the current working directory and exit if it can't find this file. Here is an example of the contents of input.nex

ASCII File Contents

begin paup;
  set crit=likelihood;
  lset nst=2 tratio=4.71 rates=gamma shape=0.4036;
end;

Related Material

PAUP Documentation

• PAUP Command Reference