phylopypruner 0.5.1

tree-based orthology inference

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:[e-mail]).

## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis)

• [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/about-phylopypruner)

• Tutorial

• [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation)

• [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data)

• [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files)

• [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods)

• [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