Metadata-Version: 1.1
Name: pyasr
Version: 0.4.2
Summary: Ancestral sequence reconstruction using Python
Home-page: https://github.com/Zsailer/pyasr
Author: Zachary Sailer
Author-email: zachsailer@gmail.com
License: BSD 3
Description-Content-Type: UNKNOWN
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
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
