Metadata-Version: 2.1
Name: getphylo
Version: 0.1.0
Summary: a python package for automated generation of heuristic phylogenetic trees from genbank files
Home-page: https://github.com/DrBoothTJ/getphylo
Author: Thomas J. Booth
Author-email: thoboo@biosustain.dtu.dk
License: GNU General Public License v3.0
Description: # getphylo: GEnbank To PHYLOgeny
        a python package for automated generation of heuristic phylogenetic trees from genbank files
        
        ## Description
        getphylo was designed to automatically build multi-locus phylogenetic trees from GenBank files. The workflow consists of the following steps: i) extract protein coding sequences; ii) screen for suitable markers; iii) align individual marker sequences and create a combined alignment; and iv) produce a tree from the combined alignment. Please see the 'parameters' section below for a full list of parameters.
        
        ## Installation
        
        The easiest way to install `getphylo` is using the command: 
        
        `pip install getphylo`
        
        This will fetch and install the latest version from: https://pypi.org/project/getphylo/
        
        For full installation instructions, please see the [getphylo wiki](https://github.com/drboothtj/getphylo/wiki/Installation).
        
        **Important:** getphylo requires DIAMOND, MUSCLE and FastTree2 to be installed to work correctly. These must be installed manually. Further instructions are [availiable on the wiki](https://github.com/drboothtj/getphylo/wiki/Installation).
        
        ## Quick-start
        This package has been designed to be as easy to run as possible. Simply navigate to a working directory containing .gbk files and input:
        
        `getphylo`
        
        This will run the software with default settings.
        
        A full list of options and flags can be viewed with:
        
        `getphylo -h`
        
        A [full list of parameters](https://github.com/drboothtj/getphylo/wiki/Parameter-List) and [further usage examples](https://github.com/drboothtj/getphylo/wiki/Advanced-Usage-(Case-Studies)) are availiable on the wiki.
        
        ## Example Analysis and Datasets
        See the ´example_data´ folder in this directory for three example trees produced by `getphylo`.
        
        1. A phylogeny of bacterial genomes
        2. A phylogeny of eukaryotic mitochondrial genomes
        3. A phylogeny of a biosynthetic super cluster
        4. A phylogeny of primate genomes
        
Platform: UNKNOWN
Requires-Python: >=3.7
Description-Content-Type: text/markdown
