Python API for managing a phylogenetics project
# Python API for managing a phylogenetics project
Phylogenetics is a minimal Python API for doing phylogenetics. It manages the annoying aspects of phylogenetics (i.e. file conversion) for you and lets you focus on exploring and interpreting the data.
**Note** The `phylogenetics` package has been completely rewritten between v0.3 and v0.4. v0.3 is now deprecated and no longer maintained. v0.4 has significantly simplified the API. I hope you enjoy it.
## The Basics
The main entry-point to the API is the `Project` object, which acts as a container object for all pieces of a
phylogenetics project. Below is an example of how to use the `Project` class.
from phylogenetics import TreeProject
# Initialize a project class
project = TreeProject(project_dir='project')
project.read_data(dtype='tips', path='alignment.fasta', schema='fasta')
# Run PhyML to construct a phylogenetic
# tree by maximum likelihood.
# Reconstruct ancestral sequences.
<img src="docs/_images/jlab.png" align="middle">
`phylogenetics` has been rewritten from scratch. The version on PyPi is outdated
and will not work with the new version. For now, install from source.
git clone https://github.com/Zsailer/phylogenetics
pip install -e .
`phylogenetics` manages phylogenetics data. Currently, it doesn't do any of the phylogenetic calculations itself. For this, use external tools like:
1. `cdhit` - clustering redundant sequences
2. `msaprobs` - multiple sequence alignment software
3. `phyml` - building maximum likelihood trees
4. `paml` - reconstructing ancestors
`phylogenetics` is built on top of following python stack:
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