Skip to main content
Help us improve PyPI by participating in user testing. All experience levels needed!

Ancestral sequence reconstruction using Python

Project description


**Ancestral Sequence Reconstruction in Python**

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

Under the hood, PyASR wraps [PAML]( ("Phylogenetic Analysis by Maximum Likelihood"). It then uses [PhyloPandas]( to store the results in human-readable DataFrames.

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

## Basic Usage

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.

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
pip install -e .

## Dependencies

The actual reconstruction calculation are done using [PAML]( 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

Release history Release notifications

This version
History Node


History Node


History Node


History Node


Download files

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

Filename, size & hash SHA256 hash help File type Python version Upload date
pyasr-0.4.3-py2.py3-none-any.whl (39.0 kB) Copy SHA256 hash SHA256 Wheel py2.py3 Nov 8, 2017
pyasr-0.4.3.tar.gz (33.4 kB) Copy SHA256 hash SHA256 Source None Nov 8, 2017

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page