🌲 PhyloDM

Efficient calculation of pairwise phylogenetic distance matrices.

PhyloDM is a high-performance library that converts a phylogenetic tree into pairwise distance matrix. It is designed to run on use minimal memory (<100 MB), and takes seconds to compute large trees (>20,000 taxa), whereas other libraries may take hours and use hundreds of GB of memory.

PhyloDM is written in Rust and is exposed to Python via the Python PyO3 API. This means it can be used in either Python or Rust, however, the documentation is written for use in Python.

⚙ Installation

Requires Python 3.7+

Conda (recommended)

shell conda install -c b bioconda phylodm

PyPI (alternative)

Pre-compiled binaries are packaged for most 64-bit platforms running Python 3.9 and 3.10. If you are running a different Python version, then you need to have Rust installed to compile the binaries.

shell python -m pip install phylodm

🐍 Quick-start

A pairwise distance matrix can be created from either a Newick file, or DendroPy tree.

```python from phylodm import PhyloDM

PREPARATION: Create a test tree

with open('/tmp/newick.tree', 'w') as fh: fh.write('(A:4,(B:3,C:4):1);')

1a. From a Newick file

pdm = PhyloDM.loadfromnewick_path('/tmp/newick.tree')

1b. From a DendroPy tree

import dendropy tree = dendropy.Tree.getfrompath('/tmp/newick.tree', schema='newick') pdm = PhyloDM.loadfromdendropy(tree)

2. Calculate the PDM

dm = pdm.dm(norm=False) labels = pdm.taxa()

""" /------------[4]------------ A + | /---------[3]--------- B ---[1]---+ ------------[4]------------- C

labels = ('A', 'B', 'C') dm = [[0. 8. 9.] [8. 0. 7.] [9. 7. 0.]] """ ```

Accessing data

The dm method generates a symmetrical NumPy matrix and returns a tuple of keys in the matrix row/column order.

```python

Calculate the PDM

dm = pdm.dm(norm=False) labels = pdm.taxa()

""" /------------[4]------------ A + | /---------[3]--------- B ---[1]---+ ------------[4]------------- C

labels = ('A', 'B', 'C') dm = [[0. 8. 9.] [8. 0. 7.] [9. 7. 0.]] """

e.g. The following commands (equivalent) get the distance between A and B

dm[0, 1] # 8 dm[labels.index('A'), labels.index('B')] # 8 ```

Normalisation

If the norm argument of dm is set to True, then the data will be normalised by the sum of all edges in the tree.

⏱ Performance

Tests were executed using the scripts/phylodm_perf.py script with 10 trials.

These tests demonstrate that PhyloDM is more efficient than DendroPy's phylogenetic distance matrix when there are over 500 taxa in the tree. If there are less than 500 taxa, then use DendroPy for all of the great features it provides.

With 10,000 taxa in the tree, each program uses approximately: * PhyloDM = 4 seconds / 40 MB memory * DendroPy = 17 minutes / 22 GB memory