Metadata-Version: 1.1
Name: phylogenetics
Version: 0.4
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
        
        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 v0.3 is now deprecated and no longer maintained.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.
        
        ## The Basics
        
        The main entry-point to the API is the `Project` object, which acts as a container object for all pieces of a
        phylogenetics project. Below is an example of how to use the `Project` class.
        
        ```python
        # Imports
        from phylogenetics import TreeProject
        
        # Initialize a project class
        project = TreeProject(project_dir='project')
        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.
        project.run_reconstruction(alpha=1.2)
        ```
        
        <img src="docs/_images/jlab.png" align="middle">
        
        ## Installation
        
        `phylogenetics` has been rewritten from scratch. The version on PyPi is outdated
        and will not work with the new version. For now, install from source. 
        ```
        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:
        
        1. `cdhit` - clustering redundant sequences
        2. `msaprobs` - multiple sequence alignment software
        3. `phyml` - building maximum likelihood trees
        4. `paml` - reconstructing ancestors
        
        `phylogenetics` is built on top of following python stack:
        
        1. Pandas 
        2. Biopython
        3. DendroPy
        4. ToyTree
        5. PhyloPandas
        
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
