phylopypruner 0.5.2

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]).


Figure 1. An overview of a tree-based orthology inference approach. First, sequences from different species are clustered together based on an all-versus-all BLAST, followed by Markov clustering. Each node in the cluster corresponds to a sequence and each edge corresponds to a similarity score. Homologous groups are then aligned and a phylogenetic tree is inferred from the alignment. From this tree, orthologous groups can be identified and paralogs are pruned away.

## 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)

• [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