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        "author": "Felix Thalen",
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            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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        "description": "<img src=\"https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/ppp_logo.png\" alt=\"ppp_logotype\" width=\"350\"/>\n\n## About\n\n*Orthologs* are genes that are related through a speciation event, while\n*paralogs* are genes that are related through a gene duplication event.\nAccurate identification of orthologs is a prerequisite for phylogenomics, since\nincluding genes that diverged because of a gene duplication event for species\ntree inference can cause an erroneous inference of speciation nodes, due to\ndisparencies between individual gene trees and the species tree. Unfortunately,\ncontaminants present in even a single taxon can cause a tree-based orthology\ninference method to erroneuosly infer paralogy and unnecessarily exclude\nsequences.\n\nPhyloPyPruner is a Python package for phylogenetic tree-based orthology\ninference, using the species overlap method. It uses trees and alignments\ninferred from the output of a graph-based orthology inference approach, such\nas [OrthoMCL](https://www.ncbi.nlm.nih.gov/pubmed/12952885),\n[OrthoFinder](https://www.ncbi.nlm.nih.gov/pubmed/26243257) or\n[HaMStR](https://www.ncbi.nlm.nih.gov/pubmed/19586527), in order to obtain sets\nof sequences that are 1:1 orthologous. In addition to algorithms seen in\npre-existing tree-based tools (for example,\n[PhyloTreePruner](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825643/),\n[UPhO](https://academic.oup.com/mbe/article/33/8/2117/2578877),\n[Agalma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840672/) or\n[Phylogenomic Dataset\nReconstruction](https://www.ncbi.nlm.nih.gov/pubmed/25158799)), this package\nprovides new methods for reducing potential contamination.\n\n![proteomes2orthologs](https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/proteomes2orthologs.png)\n\n**Figure 1.** A rough overview of a tree-based orthology inference approach.\n\n## Quick installation\n\nThe easiest way to install PhyloPyPruner is by using the package manager for\nPython, [pip](https://pypi.org/project/pip/):\n\n```bash\npip install phylopypruner # install for all users\npip install --user phylopypruner # install for the current user only\n```\n\nOnce installed, the program is located within `$HOME/.local/bin`. Depending on\nyour OS, you might have to add the directory to your `$PATH` to avoid typing\nthe entire path. Once in your path, you run the program like this:\n\n```bash\nphylopypruner\n```\n\n## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis)\n\n1. [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/about-phylopypruner)\n2. [Tutorial](https://gitlab.com/fethalen/phylopypruner/wikis/tutorial#phylopypruner-tutorial)\n3. [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation)\n4. [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data)\n5. [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files)\n6. [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods)\n7. [Options](https://gitlab.com/fethalen/phylopypruner/wikis/options)\n\n## Cite\n\nOur manuscript is still in preparation, it will be posted here once a preprint\nof the article is available.\n\n\u00a9 [Kocot Lab](https://www.kocotlab.com/) 2019\n\n\n",
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