Metadata-Version: 1.1
Name: phylogenetics
Version: 0.4.1
Summary: Python API for managing a phylogenetics project
Home-page: https://github.com/Zsailer/phylogenetics
Author: Zachary Sailer
Author-email: zachsailer@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: 
        # Python API for managing a phylogenetics project
        
        [![Documentation Status](http://readthedocs.org/projects/phylogenetics/badge/?version=latest)](http://phylogenetics.readthedocs.io/en/latest/?badge=latest)
        
        
        Phylogenetics is a minimal Python API for doing phylogenetics. It manages the annoying aspects of phylogenetics (i.e. file conversion) for you and lets you focus on exploring and interpreting the data.  
        
        **Note** The `phylogenetics` package has been completely rewritten between v0.3 and v0.4. v0.3 is now deprecated and no longer maintained. v0.4 has significantly simplified the API. I hope you enjoy it.
        
        ## Basic Example
        
        The main object in phylogenetics is the `TreeProject`. Start by initializing the `TreeProject`
        object, pointing to a directory where you'd like to store all the phylogenetic data/output. 
        
        ```python
        # Imports
        from phylogenetics import TreeProject
        
        # Initialize a project class
        project = TreeProject(project_dir='project')
        ```
        
        Then, add an alignment (using any file schema you'd like). These sequences will be the
        tips of your tree. You can now begin building trees and reconstructing ancestral sequences.
        
        ```python
        project.read_data(dtype='tips', path='alignment.fasta', schema='fasta')
        
        # Run PhyML to construct a phylogenetic 
        # tree by maximum likelihood.
        project.run_tree()
        
        # Reconstruct ancestral sequences using default settings.
        project.run_reconstruction()
        ```
        
        `phylogenetics` imports the `toytree` library to quickly plot trees in Jupyter Notebooks.
        You can quickly view your tree anytime using the `draw_tree` method. 
        ```python
        project.draw_tree(width=700,
            tip_labels='id',
            tip_labels_align=True,
            use_edge_lengths=True,
            node_labels='id')
        ``` 
        
        <img src="docs/_images/jlab.png" align="middle">
        
        ## Installation
        
        Install from PyPi:
        ```
        pip install phylogenetics
        ```
        
        To install a development version:
        ```
        git clone https://github.com/Zsailer/phylogenetics
        cd phylogenetics
        pip install -e .
        ```
        
        ## Dependencies
        
        `phylogenetics` manages phylogenetics data. Currently, it doesn't do any of the phylogenetic calculations itself. For this, use external tools like:
        
        3. [PhyML](http://www.atgc-montpellier.fr/phyml/) - building maximum likelihood trees.
        4. [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) - reconstructing ancestors.
        
        `phylogenetics` is built on top of following python stack:
        
        1. Pandas 
        2. Biopython
        3. DendroPy
        4. ToyTree
        5. PhyloPandas
        6. PyASR
        
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
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
