README.md

In BIONF/PhyloProfile: PhyloProfile

PhyloProfile

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
• Input Data
• Walkthrough & Examples
• Bugs
• Acknowledgements
• License
• How-To Cite
• 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:

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:

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:

if (!requireNamespace("devtools"))
    install.packages("devtools")
devtools::install_github("BIONF/PhyloProfile", INSTALL_opts = c('--no-lock'))

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:

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:

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, https://doi.org/10.1093/bioinformatics/bty225

or use the citation function in R CMD to have it directly in BibTex or LaTeX format

citation("PhyloProfile")

Contact

Vinh Tran [e-mail]

BIONF/PhyloProfile documentation built on Nov. 7, 2024, 8:31 p.m.