The sumtrees program summarize non-parameteric bootstrap or Bayesian posterior probability support for splits or clades on phylogenetic trees.

References:

• Sukumaran, J. and Mark T. Holder. DendroPy: A Python library for phylogenetic computing.Bioinformatics.2010.26: 1569-1571. PubMed |  Journal

• sumtrees Mainsite:Mainsite

• Module Name: sumtrees (see the modules page for more information)
• Current sumtrees command lines could be run as:

  	sumtrees.py
  	

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load sumtrees
[user@cn3144 ~]$ sumtrees.py --help
[user@cn3144 ~]$ sumtrees.py --min-clade-freq=0.95 --burnin=200 --output-tree-filepath=result.tre treefile1.tre treefile2.tre treefile3.tre
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. sumtrees.sh). For example:

#!/bin/bash
set -e
module load sumtrees
sumtrees.py -m4 -f0.95 -b200 -o result.tre treefile1.tre treefile2.tre treefile3.tre treefile4.tre

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=2g sumtrees.sh

Create a swarmfile (e.g. sumtrees.swarm). For example:

cd dir1;sumtrees.py -f0.95 -b200 -o result.tre treefile1.tre treefile2.tre treefile3.tre
cd dir2;sumtrees.py --summary-target=mcct --burnin=200 --support-as-labels --output-tree-filepath=result2.tre treefile1.tre treefile2.tre treefile3.tre

Submit this job using the swarm command.

swarm -f sumtrees.swarm [-t #] [-g #] --module sumtrees