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# PhyloProfile [![Bioconductor](]( [![install with bioconda](]( [![published in: Bioinformatics](]( [![presented at: GCB2018](]( [![poster at: SMBE2019](]( [![BioC status](]( ![]( [Click here for the full PDF version of the BOSC2017 poster]( *PhyloProfile* is an R package that comes together with a *Shiny*-based tool for integrating, visualizing and exploring multi-layered [phylogenetic profiles]( Alongside the presence/absence patterns of [orthologs]( across large [taxon]( collections, *PhyloProfile* allows the integration of any two additional information layers. These complementary data, like [sequence similarity]( between orthologs, similarities in their [domain architecture](, or differences in [functional annotations]( enable a more informed interpretation of phylogenetic profiles. By utilizing the [NCBI taxonomy](, *PhyloProfile* can dynamically collapse taxa into higher [systematic groups]( 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. *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]( and [core gene]( sets facilitates the exploration and analysis of large phylogenetic profiles. Take a look at [the functionality]( of *PhyloProfile* and [explore the installation-free online version]( to learn more. # Table of Contents * [Installation & Usage](#installation--usage) * [Input Data](#input-data) * [Walkthrough & Examples](#walkthrough--examples) * [Bugs](#bugs) * [Acknowledgements](#acknowledgements) * [License](#license) * [How-To Cite](#how-to-cite) * [Contact](#contact) # Installation & Usage *PhyloProfile* requires the latest version of [R]( (check for required R version [here]( Please install or update R on your computer before continue. * [R for Linux]( * [R for Mac OS]( * [R for Windows]( Then start R to install and use *PhyloProfile*. ## Using BiocManager *PhyloProfile* is available at [Bioconductor]( (require Bioc version ≥ 3.14). To install *PhyloProfile*, start R and enter: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PhyloProfile") ``` To install the development version of PhyloProfile, please use the [devel version]( of Bioconductor: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version='devel') BiocManager::install("PhyloProfile") ``` or *install the dev version of *PhyloProfile* from our github repository using __[devtools](* ## Using devtools The dev version of *PhyloProfile* can be installed from this github repository using `devtools`: ```r if (!requireNamespace("devtools")) install.packages("devtools") devtools::install_github("BIONF/PhyloProfile", INSTALL_opts = c('--no-lock'), build_vignettes = TRUE) ``` ## Using Conda *PhyloProfile* can also be installed within a [conda]( environment. First, add [bioconda]( to the list of your conda channels: ``` conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge ``` then install *PhyloProfile* using the standard `conda install` command: ``` conda install bioconductor-phyloprofile ``` This 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)* ## Start PhyloProfile's Shiny app From the R terminal, enter: ```r library(PhyloProfile) runPhyloProfile() ``` Check your web browser, *PhyloProfile* will be displayed there ;-) For the first time running, the tool will download a [pre-caculated taxonomy data]( Please be patient until you see a message for uploading input files. _**Please check our [detailed instructions]( if you encounter any problems while installing and starting the program.**_ # Input Data *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. We described all suppported input formats in section [Input Data]( in our [PhyloProfile's Wiki]( # Walkthrough & Examples Read the [walkthrough slides]( to explore the functionality of the *PhyloProfile* GUI. Check the vignette for learning how to use PhyloProfile's functions in some specific use-cases: ```r browseVignettes("PhyloProfile") ``` # Bugs Any [bug reports or comments, suggestions]( are highly appreciated. Please [open an issue on GitHub]( or be in touch via email. # Acknowledgements We would like to thank 1) [Bastian]( for the great initial idea and his kind support, 2) Members of [Ebersberger group]( for many valuable suggestions and ...bug reports :) # Contributors * [Vinh]( * [Bastian]( * [Carla]( # License This tool is released under [MIT license]( # How-To Cite Ngoc-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, or use the citation function in R CMD to have it directly in BibTex or LaTeX format ```r citation("PhyloProfile") ``` # Contact Vinh Tran