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PhyloProfile\n[![Bioconductor](https://img.shields.io/badge/available%20at-Bioconductor-orange)](https://bioconductor.org/packages/PhyloProfile)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-phyloprofile/README.html)\n[![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/bty225)\n[![presented at: GCB2018](https://img.shields.io/badge/presented%20at-GCB2018-green.svg?style=flat)](http://gcb2018.de)\n[![poster at: SMBE2019](https://img.shields.io/badge/poster%20at-SMBE2019-green)](https://f1000research.com/posters/6-1782)\n[![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/PhyloProfile.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/PhyloProfile)\n\n![](https://github.com/BIONF/phyloprofile-data/blob/gh-pages/www/posterSub.png)\n[Click here for the full PDF version of the BOSC2017 poster](https://f1000research.com/posters/6-1782)\n\n*PhyloProfile* is an R package that comes together with a *Shiny*-based tool for integrating, visualizing and exploring multi-layered [phylogenetic profiles](https://en.wikipedia.org/wiki/Phylogenetic_profiling).\n\nAlongside the presence/absence patterns of [orthologs](https://en.wikipedia.org/wiki/Homology_(biology)) across large [taxon](https://en.wikipedia.org/wiki/Taxon) collections, *PhyloProfile* allows the integration of any two additional information layers. These complementary data, like [sequence similarity](https://en.wikipedia.org/wiki/Sequence_alignment) between orthologs, similarities in their [domain architecture](https://www.ncbi.nlm.nih.gov/pubmed/20221914), or differences in [functional annotations](https://en.wikipedia.org/wiki/Protein_function_prediction) enable a more informed interpretation of phylogenetic profiles.\n\nBy utilizing the [NCBI taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy), *PhyloProfile* can dynamically collapse taxa into higher [systematic groups](https://en.wikipedia.org/wiki/Taxonomy_(biology)). This enables rapidly changing the resolution from the comparative analyses of proteins in individual species to that of entire kingdoms or even domains without changes to the input data.\n\n*PhyloProfile* furthermore allows for a dynamic filtering of profiles – taking the taxonomic distribution and the additional information layers into account. This, along with functions to estimate [the age of genes](http://www.cell.com/trends/genetics/fulltext/S0168-9525(13)00111-X) and [core gene](https://en.wikipedia.org/wiki/Pan-genome) sets facilitates the exploration and analysis of large phylogenetic profiles.\n\nTake a look at [the functionality](https://github.com/BIONF/PhyloProfile/wiki/Functionality) of *PhyloProfile* and [explore the installation-free online version](http://applbio.biologie.uni-frankfurt.de/phyloprofile/) to learn more.\n\n# Table of Contents\n* [Installation \u0026amp; Usage](#installation--usage)\n* [Input Data](#input-data)\n* [Walkthrough \u0026amp; Examples](#walkthrough--examples)\n* [Bugs](#bugs)\n* [Acknowledgements](#acknowledgements)\n* [License](#license)\n* [How-To Cite](#how-to-cite)\n* [Contact](#contact)\n\n# Installation \u0026 Usage\n*PhyloProfile* requires the latest version of [R](https://cran.r-project.org) (check for required R version [here](https://bioconductor.org/packages/PhyloProfile)). Please install or update R on your computer before continue.\n\n* [R for Linux](https://cran.r-project.org/bin/linux/)\n* [R for Mac OS](https://cran.r-project.org/bin/macosx/)\n* [R for Windows](https://cran.r-project.org/bin/windows/base/)\n\nThen start R to install and use *PhyloProfile*.\n\n## Using BiocManager\n*PhyloProfile* is available at [Bioconductor](https://bioconductor.org/packages/PhyloProfile) (require Bioc version ≥ 3.14). To install *PhyloProfile*, start R and enter:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"PhyloProfile\")\n```\n\nTo install the development version of PhyloProfile, please use the [devel version](https://bioconductor.org/developers/how-to/useDevel/) of Bioconductor:\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(version='devel')\nBiocManager::install(\"PhyloProfile\")\n```\n\nor\n*install the dev version of *PhyloProfile* from our github repository using __[remotes](https://cran.r-project.org/web/packages/remotes/index.html)__.*\n\n## Using remotes package\nThe dev version of *PhyloProfile* can be installed from this github repository using `remotes`:\n\n```r\nif (!requireNamespace(\"remotes\"))\n    install.packages(\"remotes\")\nremotes::install_github(\"BIONF/PhyloProfile\")\n```\n\n## Using Conda\n*PhyloProfile* can also be installed within a [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) environment. First, add [bioconda](https://bioconda.github.io/user/install.html#set-up-channels) to the list of your conda channels:\n```\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\n```\nthen install *PhyloProfile* using the standard `conda install` command:\n```\nconda install bioconductor-phyloprofile\n```\n\nThis installation step can take a while regardless of the method used, as all necessary dependencies will be downloaded and installed automatically. *(Note: Depending on your system this sometimes fails, please check the console log for error messages concerning the dependency installation)*\n\n## Start PhyloProfile's Shiny app\n\nFrom the R terminal, enter:\n```r\nlibrary(PhyloProfile)\nrunPhyloProfile()\n```\nCheck your web browser, *PhyloProfile* will be displayed there ;-) For the first time running, the tool will download a [pre-caculated taxonomy data](https://github.com/BIONF/phyloprofile-data). Please be patient until you see a message for uploading input files.\n\n_**Please check our [detailed instructions](https://github.com/BIONF/PhyloProfile/wiki/Installation) if you encounter any problems while installing and starting the program.**_\n\n# Input Data\n*PhyloProfile* can read a number of different input files, including multi-FASTA files, regular tab-separated files, OMA ID lists or *OrthoXML* files. The additional information layers can be embedded in the OrthoXML or be provided separately as tab-separated files.\n\nWe described all suppported input formats in section [Input Data](https://github.com/BIONF/PhyloProfile/wiki/Input-Data) in our [PhyloProfile's Wiki](https://github.com/BIONF/PhyloProfile/wiki).\n\n# Walkthrough \u0026 Examples\nRead the [walkthrough slides](https://github.com/BIONF/PhyloProfile/wiki/Walkthrough) to explore the functionality of the *PhyloProfile* GUI.\n\nCheck the vignette for learning how to use PhyloProfile's functions in some specific use-cases:\n```r\nbrowseVignettes(\"PhyloProfile\")\n```\n\n# Bugs\nAny [bug reports or comments, suggestions](https://github.com/BIONF/PhyloProfile/blob/master/CONTRIBUTING.md) are highly appreciated. Please [open an issue on GitHub](https://github.com/BIONF/PhyloProfile/issues/new) or be in touch via email.\n\n# Acknowledgements\nWe would like to thank\n1) [Bastian](https://github.com/gedankenstuecke) for the great initial idea and his kind support,\n2) Members of [Ebersberger group](http://www.bio.uni-frankfurt.de/43045195/ak-ebersberger) for many valuable suggestions and ...bug reports :)\n\n# Contributors\n* [Vinh](https://github.com/trvinh)\n* [Bastian](https://github.com/gedankenstuecke)\n* [Carla](https://github.com/CarlaMoelbert)\n\n# License\nThis tool is released under [MIT license](https://github.com/BIONF/PhyloProfile/blob/master/LICENSE).\n\n# How-To Cite\nVinh Tran, Ingo Ebersberger, PhyloProfile v2: Scalable Exploration of Multilayered Phylogenetic Profiles via Dimensionality Reduction, 2025, Preprint available at arXiv: https://doi.org/10.48550/arXiv.2504.19710.\n  \nNgoc-Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger, PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages 3041–3043, https://doi.org/10.1093/bioinformatics/bty225\n\nor use the citation function in R CMD to have it directly in BibTex or LaTeX format\n```r\ncitation(\"PhyloProfile\")\n```\n# Contact\nVinh Tran\ntran@bio.uni-frankfurt.de\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionf%2Fphyloprofile","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionf%2Fphyloprofile","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionf%2Fphyloprofile/lists"}