Treemmer

Python tool to reduce size and redundancy of phylogenetic datasets

Here you find the software, the data and scripts used in the manuscript (Influenza_data, MTB_data and stochastic_component), and a short tutorial on fine tuning the behaviour of Treemmer with the pruning options.

Installation

From version 0.3 Treemmer is compatible with both python 2 and python 3

You need to install the following dependencies:

ETE3

Joblib

Numpy

Matplotlib

Use with singularity

Treemmer can be used with singularity (instructions for installation here).

For example:

• download the image of the container:

singularity pull --arch amd64 library://fmenardo/treemmer/treemmer:0.3

• build the container

singularity build --sandbox treemmer_sb/ treemmer_0.3.sif

• run Treemmer

singularity exec treemmer_sb/ python3 /Treemmer_v0.3.py -h

Basic usage

Plot relative tree length decay.

python3 Treemmer_v0.3.py tree_file.nwk

Prune tree until the realative tree length is 90% of starting tree.

python3 Treemmer_v0.3.py tree_file.nwk -RTL 0.9

Prune tree down to 100 tips.

python3 Treemmer_v0.3.py tree_file.nwk -X 100

Citation

If you use Treemmer please cite:

Menardo et al. (2018). Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics 19:164.

https://doi.org/10.1186/s12859-018-2164-8.

Check also treemmer-animate, a script by Thomas Hackl to visualize the "treemming" process: https://github.com/thackl/treemmer-animate