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Description:

pyasr 0.6.1

PyASR
Ancestral Sequence Reconstruction in Python
PyASR offers a modern Python interface to PAML ("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
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. 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