jharman25 / phylogenetics

A Python API for managing phylogenetics projects

Phylogenetics

A Python API for interactive phylogenetics

Phylogenetics is a minimal Python API that makes phylogenetics interactive and reproducible. It's main purpose is to take you from a multiple sequence alignment to a set of ancestral sequences.

Basic Example

Initialize a PhylogeneticsProject object, add your alignment, and analyze your tree all in the Jupyter notebook.

# Imports
from phylogenetics import PhylogeneticsProject

# Initialize a project class
project = PhylogeneticsProject(project_dir='project')

# Add tips data or alignment.
project.read_data(dtype='tips', path='alignment.fasta', schema='fasta')

# Compute phylogenetic tree and ancestors.
project.compute_tree()
project.compute_ancestors()

Installation

Install from PyPi:

pip install phylogenetics

To install a development version:

git clone https://github.com/Zsailer/phylogenetics
cd phylogenetics
pip install -e .

Dependencies

Phylogenetics manages phylogenetics data. Currently, it doesn't do any of the phylogenetic calculations itself. For this, it uses wraps external tools like:

3. PhyML: for building maximum likelihood trees. (http://www.atgc-montpellier.fr/phyml/)
4. PAML: for reconstructing ancestors. http://abacus.gene.ucl.ac.uk/software/paml.html)

Phylogenetics is built on top of following python stack:

1. Pandas
2. Biopython
3. DendroPy
4. ToyTree
5. PhyloPandas
6. PyASR