https://github.com/zsailer/pyasr

Ancestral Sequence Reconstruction in Python
https://github.com/zsailer/pyasr

evolution pandas phylogenetics python

Last synced: about 2 months ago
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Ancestral Sequence Reconstruction in Python

• Host: GitHub
• URL: https://github.com/zsailer/pyasr
• Owner: Zsailer
• License: bsd-3-clause
• Created: 2017-10-26T15:59:03.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-05-09T15:30:20.000Z (over 5 years ago)
• Last Synced: 2024-04-29T22:43:26.748Z (8 months ago)
• Topics: evolution, pandas, phylogenetics, python
• Language: Python
• Size: 678 KB
• Stars: 11
• Watchers: 1
• Forks: 8
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# PyASR

**Ancestral Sequence Reconstruction in Python**

PyASR offers a modern Python interface to [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) ("Phylogenetic Analysis by Maximum Likelihood")--tuned specifically for reconstruction

ancestral protein/DNA sequences.

**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.



## 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