mulberrytree

This script produces publication-quality figures from Newick tree files, collapsing user-defined groups of leaves.

Install dependencies

# Clone repository
git clone https://github.com/danieltamarit/mulberrytree.git
cd mulberrytree

# Install basic dependencies
conda env create -f envs/conda_env_base.yml
conda activate mulberry

Options

   -h     Print this help
   -t     Input tree in Newick format (required)
   -g     Group information in tsv format
            (Column 1: Leaf name; Column 2: Group name)
   -c     Color information in tsv format
            (Column 1: Group name; Column 2: R-readable color)
   -m     Midpoint root
   -o     Prefix for output files
   -w     Width for collapsed and uncollapsed PDF
   -W     Width for collapsed PDF
   -Y     Width for uncollapsed PDF
   -l     Interpret group name from leaf name
   -s     Separator for group interpretation from leaf (default: \"|\")
   -x     Text or regular expression to be ignored as leaf name suffix
   -i     Text or regular expression to be ignored as leaf name prefix
            when assessing group monophyly
   -T     Number of threads used for tree processing (default: 1)
            Note: optimal speed often reached with 1-2 threads

Basic usage

mulberrytree -h
mulberrytree -t <newick_tree> -g <leaf_classification> -c <group_colors>
mulberrytree -t <newick_tree> -l -s "<separator>"

Example runs:

mulberrytree -t example/a_treeSimple.nwk -g example/b_taxa.tsv -c example/c_colorGroups.tsv -x "_[0-9]+G"
mulberrytree -t example/a_treeSimple2_sepPipe.nwk -l
mulberrytree -t example/a_treeSimple3_sepUnderscores.nwk -l -s "___"

The name "mulberrytree" is a wink to figtree, a great, interactive visualisation software I have spent too many hours of my life using, and for which I often hoped a less manual equivalent existed.