Metadata-Version: 2.1
Name: getphylo
Version: 0.0.2
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
        a python package for automated generation of heuristic phylogenetic trees from genbank files
        
        ## Description
        WIP
        
        ## Installation
        
        **Important:** The following intructuons are for Linux and assume you have Python and pip installed already. For installation on different systems, please see the links provided for this individual dependences.
        
        ### 1. Installation of getphylo
        
        #### Installation with PyPI
        Coming soon!
        
        #### Manual Installation
        
        If you want to install `getphylo` manually, you can do so by cloning this repository.
        
        `git clone https://github.com/DrBoothTJ/getphylo`
        `cd getphylo`
        `python setup.py install`
        
        ### 2. Installation of dependences
        
        **Important:** Getphylo requires DIAMOND, MUSCLE and FastTree2 to be installed to work correctly. These must be installed manually. BioPython should be installed automatically. Below are instructions to install each dependency:
        
        #### Installing DIAMOND
        
        You can install DIAMOND with the following command:
        
        `sudo apt install diamond-aligner`
        
        Further instructions for installing DIAMOND can be found, here: https://github.com/bbuchfink/diamond/wiki/2.-Installation.
        
        
        #### Installing MUSCLE
        
        You can install MUSCLE with the following command:
        
        WIP
        
        
        #### Installing FastTree2
        
        You can install FastTree2 with the following command:
        
        `sudo apt install fasttree`
        
        Further instructions for installing FastTree2 can be found, here: http://www.microbesonline.org/fasttree/.
        
        #### Installing BioPython
        
        If you installed `getphylo` using PyPI, BioPython should be installed automatically. If you installed `getphylo` manually, you will need to install BioPython yourself.
        This can be done using the command:
        
        `pip install biopython`
        
        Further instructions for installing FastTree2 can be found, here: https://biopython.org/wiki/Download.
        
        
        ## Usage
        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 on default settings and output all alignments and trees.
        
        There may be occasions where you need to change the default settings. A full list of options and flags can be viewed with:
        
        `getphylo -h`
        
        Below is a breif describtion of each flag.
        
        ### Flags
        WIP
        
        ## Examples
        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
