Metadata-Version: 2.1
Name: phylopypruner
Version: 0.6.6
Summary: tree-based orthology inference
Home-page: https://gitlab.com/fethalen/phylopypruner
Author: Felix Thalen
Author-email: fe1430th-s@student.lu.se
License: MIT
Keywords: orthology inference,orthologs,tree-based,phylogenetics,phylogenomics,orthology
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown

<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


