Metadata-Version: 2.1
Name: phylopypruner
Version: 0.8.2
Summary: tree-based orthology inference
Home-page: https://gitlab.com/fethalen/phylopypruner
Author: Felix Thalen
Author-email: fe1430th-s@student.lu.se
License: GPL 3
Description: <img src="https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/ppp_logo.png" alt="ppp_logotype" width="350"/>
        
        ## What is PhyloPyPruner?
        
        PhyloPyPruner is a Python package for refining the output of a graph-based
        orthology inference approach such as
        [OrthoMCL](https://www.ncbi.nlm.nih.gov/pubmed/12952885),
        [OrthoFinder](https://www.ncbi.nlm.nih.gov/pubmed/26243257) or
        [HaMStR](https://www.ncbi.nlm.nih.gov/pubmed/19586527). Similar to other
        tree-based orthology inference methods (e.g.,
        [PhyloTreePruner](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825643/),
        [UPhO](https://academic.oup.com/mbe/article/33/8/2117/2578877),
        [Agalma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840672/) and
        [Phylogenomic Dataset
        Reconstruction](https://www.ncbi.nlm.nih.gov/pubmed/25158799)), it
        uses phylogenetic trees in order to obtain genes that are 1:1 orthologous. In
        addition to filters and algorithms seen in pre-existing tools, this package
        provides new methods for differentiating [contamination-like
        sequences](https://gitlab.com/fethalen/phylopypruner/wikis/About-PhyloPyPruner#contamination-like-issues-)
        from paralogs.
        
        PhyloPyPruner is under active development and I would appreciate it if you try
        this software on your own data and [leave
        feedback](mailto:felix.thalen@uni-goettingen.de).
        
        ![proteomes2orthologs](https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/proteomes2orthologs.png)
        
        **Figure 1.** A rough overview of a tree-based orthology inference approach.
        
        ## Quick installation
        
        The easiest way to install PhyloPyPruner is by using the package manager for
        Python, [pip](https://pypi.org/project/pip/):
        
        ```bash
        pip install phylopypruner # install for all users
        pip install --user phylopypruner # install for the current user only
        ```
        
        Once installed, the program is located within `$HOME/.local/bin`. Depending on
        your OS, you might have to add the directory to your `$PATH` to avoid typing
        the entire path. Once in your path, you run the program like this:
        
        ```bash
        phylopypruner
        ```
        
        ## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis)
        
        1. [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/about-phylopypruner)
        2. [Tutorial](https://gitlab.com/fethalen/phylopypruner/wikis/tutorial#phylopypruner-tutorial)
        3. [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation)
        4. [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data)
        5. [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files)
        6. [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods)
        7. [Options](https://gitlab.com/fethalen/phylopypruner/wikis/options)
        
        ## Cite
        
        Our manuscript is still in preparation, it will be posted here once a preprint
        of the article is available.
        
        © [Kocot Lab](https://www.kocotlab.com/) 2018
        
Keywords: orthology inference,orthologs,tree-based,phylogenetics,phylogenomics,orthology
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
