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Bioconductor version: Release (3.19)

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Author: Vinh Tran [aut, cre] , Bastian Greshake Tzovaras [aut], Ingo Ebersberger [aut], Carla Mölbert [ctb]

Maintainer: Vinh Tran <tran at>

Citation (from within R, enter citation("PhyloProfile")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

PhyloProfile HTML R Script
Reference Manual PDF


biocViews DataRepresentation, FunctionalPrediction, MultipleComparison, Software, Visualization
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, OmaDB, plyr, xml2, zoo, yaml
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Follow Installation instructions to use this package in your R session.

Source Package PhyloProfile_1.18.0.tar.gz
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macOS Binary (x86_64) PhyloProfile_1.18.0.tgz
macOS Binary (arm64) PhyloProfile_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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