Skip to main content

Ancestral sequence reconstruction using Python

Project description


# PyASR

**Ancestral Sequence Reconstruction in Python**

PyASR provides a simple Python interface for Ancestral Sequence Reconstruction (ASR). Easily reconstruct a set of ancestral protein/DNA sequences from a phylogenetic tree and a multiple sequence alignment without leaving Python. Check out the example below!

Under the hood, PyASR wraps [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) ("Phylogenetic Analysis by Maximum Likelihood"). It then uses [PhyloPandas](https://github.com/Zsailer/phylopandas) to store the results in human-readable DataFrames.

**NOTE:** PyASR currently only supports protein reconstructions. This is a work in progress.

## Basic Usage

```python
import phylopandas as pd
import dendropy as d
import pyasr

# Use phylopandas to read a set of ancestor.s
df_seqs = pd.read_fasta('test.fasta')

# Use dendropy to read in tree.
tree = d.Tree.get(path='tree.newick', schema='newick')

# Reconstruct nodes in tree.
tree, df_seqs, df_anc = pyasr.reconstruct(df_seqs, tree, working_dir='test', alpha=1.235)

# Write out ancestor dataframe to a CSV file.
df_anc.to_csv('ancestors.csv')
```

We can visualize the ancestors side-by-side with the tree using inside of JupyterLab
thanks to the ToyTree library.

<img src="docs/jlab-example.png" align="middle">

## Install

This package is released on PyPi. You can install using pip:
```
pip install pyasr
```

To get the development version:
```
git clone
cd
pip install -e .
```

## Dependencies

The actual reconstruction calculation are done using [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html). This requires PAML to be
installed and the `codeml`/`baseml` executables exported to your `$PATH` environment variable. Directions for installing PAML can be found on the PAML website.

The following Python dependencies are required for PyASR to work.

- Pandas
- Biopython
- PhyloPandas
- DendroPy


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyasr-0.4.2.tar.gz (33.3 kB view hashes)

Uploaded Source

Built Distribution

pyasr-0.4.2-py2.py3-none-any.whl (38.9 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page