Introduction

Phylogenetic profiles capture the presence - absence pattern of genes across species (Pellegrini et al., 1999). The presence of an ortholog in a given species is often taken as evidence that also the corresponding function is represented (Lee et al., 2007). Moreover, if two genes agree in their phylogenetic profile, it can suggest that they functionally interact (Pellegrini et al., 1999). Phylogenetic profiles are therefore commonly used for tracing functional protein clusters or metabolic networks across species and through time. However, orthology inference is not error-free (Altenhoff et al., 2016), and orthology does not guarantee functional equivalence for two genes (Studer and Robinson-Rechavi, 2009). Therefore, phylogenetic profiles are often integrated with accessory information layers, such as sequence similarity, domain architecture similarity, or semantic similarity of Gene Ontology-term descriptions.

Various approaches exist to visualize such profiles. However, there is still a shortage of tools that provide a comprehensive set of functions for the display, filtering and analysis of multi-layered phylogenetic profiles comprising hundreds of genes and taxa. To close this methodological gap, we present here PhyloProfile, an R-based tool to visualize, explore and analyze multi-layered phylogenetic profiles.

How to install PhyloProfile

To install the PhyloProfile package via Bioconductor using BiocManager:

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

To install the dev version from Bioconductor:

if (!requireNamespace("BiocManager", quitely = TRUE))
    install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("PhyloProfile")

To install the dev version from github:

if (!requireNamespace("devtools"))
    install.packages("devtools", repos = "http://cran.us.r-project.org")
devtools::install_github(
    "BIONF/PhyloProfile",
    INSTALL_opts = c('--no-lock'),
    build_vignettes = TRUE
)

Or use directly the online version at http://applbio.biologie.uni-frankfurt.de/phyloprofile/.

Input

PhyloProfile expects as a main input the phylogenetic distribution of orthologs, or more generally of homologs. This information can be complemented with domain architecture annotation and data for up to two additional annotation layers.

Beside tab delimited text and sequences in FASTA format, the tool also accepts orthoXML (Schmitt et al., 2011), or a list of OMA IDs (Altenhoff et al., 2015) as input.

Here is an example of a tab delimited input with two additional annotation layers:

geneID ncbiID orthoID FAS_F FAS_B
100136at6656 ncbi36329 100136at6656|PLAF7@36329@1|Q8ILT8|1 0.9875289 0.8427314
100136at6656 ncbi319348 100136at6656|POLVAN@319348@0|319348_0:004132|1 1.0000000 1.0000000
100136at6656 ncbi208964 100136at6656|PSEAE@208964@1|Q9I5U5|1 0.9971027 0.9971027
100136at6656 ncbi418459 100136at6656|PUCGT@418459@1|E3KFA2|1 0.9895679 0.8232540
100136at6656 ncbi10116 100136at6656|RAT@10116@1|G3V7R8|1 0.9996617 0.8541265
100136at6656 ncbi284812 100136at6656|SCHPO@284812@1|Q9USU2|1 0.9994874 0.9994874
100136at6656 ncbi35128 100136at6656|THAPS@35128@1|B8C2N6|1 0.9852370 0.7002961
100136at6656 ncbi7070 100136at6656|TRICA@7070@1|D6X457|1 1.0000000 1.0000000
100136at6656 ncbi237631 100136at6656|USTMA@237631@1|A0A0D1C927|1 0.9912998 0.6172244
100136at6656 ncbi559292 100136at6656|YEAST@559292@1|P41819|1 0.9978912 0.9978912

The WIKI accompanying PhyloProfile gives a comprehensive guide of how to format input data.

Features and capabilities

Interactive visualization and dynamic exploration of phylogenetic profiles

Together with several functions for exploring phylogenetic profiles, we provide an interactive visualization application implemented with Shiny (https://CRAN.R-project.org/package=shiny).