TIPS.md

Tips and tricks

Leveraging a high performance computer for bootstrapping

Bootstrapping is simply running mashtree several times and then quantifying how often a parent node occurs for each group of genomes. This frequency is usually displayed as a percentage at each node.

Bootstrap trees

Here is a bash loop to make 100 bootstrap trees

mkdir bootstrapTrees
export FASTA=$(ls *.fasta)
# Run the first tree without using --seed, to form your actual tree
# without bootstraps, using many threads so that it can be done before
# any of the bootstrap trees.
echo 'mashtree --numcpus $NSLOTS --mindepth 0 $FASTA' | \
  qsub -V -cwd -pe smp 1-36 -N mashtree -o mashtree.dnd -e mashtree.log

# Make 100 bootstrap trees
for i in `seq 1 100`; do 
  # The echo statement makes a short bash script, which
  # is piped to qsub
  echo '
    mashtree --numcpus $NSLOTS --mindepth 0 --seed $RANDOM $FASTA' 
  |\
    qsub -V -cwd -pe smp 1-12 -N mashtree$i -o bootstrapTrees/$i.dnd -e bootstrapTrees/$i.log; 
done;

Combine bootstrap trees

Bootstrapping with RAxML

RAxML is not a prerequisite for Mashtree, and so it might not be installed on your computer even if Mashtree is working.

cat bootstrapTrees/*.dnd > bootstrapTrees.dnd
raxmlHPC -f b -t mashtree.dnd -z bootstrapTrees.dnd -m GTRCAT -n TEST
# output file: RAxML_bipartitions.TEST
ln -sv RAxML_bipartitions.TEST bsTree.dnd # in case you want to have a sane file extension

Bootstrapping with BioPerl

This script requires bioperl, which is a prerequisite for Mashtree.

perl -MBio::TreeIO -MBio::Tree::Statistics -e '
  # Gather all the trees into an array
  for my $file(glob("bootstrapTrees/*.dnd")){
    next if(! -s $file);
    my $in=Bio::TreeIO->new(-file=>$file);
    while($tree = $in->next_tree){
      push(@tree, $tree);
    }
  }
  
  # Combine trees
  my $baseTree = Bio::TreeIO->new(-file=>"mashtree.dnd")->next_tree;
  $stats=Bio::Tree::Statistics->new; 
  my $bsTree = $stats->assess_bootstrap(\@tree,$baseTree);
  # BioPerl is very respectful about which values are IDs vs which are
  # bootstraps. However, most tree drawing programs look at IDs, so
  # we have to alter the ID
  for ($bsTree->get_nodes){
    next if($_->is_Leaf); # Do not alter leaves
    $_->id($_->bootstrap);
  }
  
  print $bsTree->as_text("newick") ."\n";
' > bsTree.dnd