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A phylogenetic profile analysis tool
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README.md

PhyloProfile

GitHub release published in: Bioinformatics poster at: BOSC2017 presented at: GCB2018 language: R license: MIT Travis-CI Build Status

Click here for the full PDF version of the BOSC2017 poster

PhyloProfile is 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

Using BiocManager

We are preparing to submit PhyloProfile to Bioconductor. Once the package is accepted, you can easily install it using BiocManager:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("PhyloProfile")

Until then please 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'), build_opts = c('--no-resave-data'))

This step can take a while, as the tool will try do download and install all necessary dependencies automatically. (Note: Depending on your system this sometimes fails, please check the console log for error messages concerning the dependency installation)

Start PhyloProfile

Simply run

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 list or OrthoXML. The additional information layers can be embedded in the OrthoXML or be provided separately.

We described all suppported input formats in section Input Data in our PhyloProfile's Wiki.

Walkthrough and 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

Code of Conduct & License

This tool is released with a Contributor Code of Conduct & 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, , bty225, 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 tran@bio.uni-frankfurt.de

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