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Treemmer

★ 56 Open GitHub ↗

Python tool to reduce size and redundancy of phylogenetic datasets

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# Treemmer
Python tool to reduce size and redundancy of phylogenetic datasets

Here you find the software, the data and scripts used in the manuscript [https://doi.org/10.1186/s12859-018-2164-8](https://doi.org/10.1186/s12859-018-2164-8), 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](https://docs.sylabs.io/guides/3.0/user-guide/installation.html)).

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

Treemmer

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