Usage

The repository TreeToCongruency provides a R script called TreeToCongruency.R to compare two Newick trees through a tanglegram and estimations of congruency metrics (Cophenetic correlations, Robinson-Foulds index, tree distances and Fowlkes-Mallows index).

Dependencies

The R script TreeToCongruency.R was prepared and tested with R version 3.6.3.

• library(dplyr)
• library(ape)
• library(dendextend)
• library(viridis)
• library(phylogram)
• library(igraph)
• library(phytools)
• library(phangorn)

Install R (Ubuntu 20.04)

1/ Update and upgrade apt-get

sudo apt-get update
sudo apt-get upgrade

2/ Check available updated R version

sudo apt-cache showpkg r-base

3/ Install updated R version

sudo apt-get install r-base

4/ Check installed R version

R --version

Install R dependencies and launch with Rscript

1/ Unpack GitHub repository and move inside

git clone https://github.com/Nicolas-Radomski/TreeToCongruency.git
cd TreeToCongruency

2/ Install R libraries

The 4.3.2 users need to install the libglpk-dev Ubuntu library to be able to install properly the igraph R library.

sudo apt-get update
sudo apt-get -y install libglpk-dev

Then, install the needed R libraries.

R
install.packages("dplyr")
install.packages("ape")
install.packages("dendextend")
install.packages("viridis")
install.packages("phylogram")
install.packages("igraph")
install.packages("phytools")
install.packages("phangorn")
quit()

3/ Launch with Rscript and different paired-trees

Rscript TreeToCongruency.R tree1.nwk tree2.nwk

Rscript TreeToCongruency.R TREE1.nwk TREE2.nwk

Install Docker image and launch with Docker

1/ Pull Docker image from Docker Hub

docker pull nicolasradomski/treetocongruency

2/ Launch with Docker and different paired-trees

docker run --name nicolas --rm -v /home/data:/data -v /home/output:/output nicolasradomski/treetocongruency:latest sh -c 'Rscript code/TreeToCongruency.R data/tree1.nwk data/tree2.nwk' > output/std.log 2>&1

sudo docker run --name nicolas --rm -v /home/data:/data -v /home/output:/output nicolasradomski/treetocongruency:latest sh -c 'Rscript code/TreeToCongruency.R data/TREE1.nwk data/TREE2.nwk' > output/std.log 2>&1

Expected output

1/ Figures of paired-trees in Tanglegram files

• Tanglegram.pdf
• Tanglegram.tiff

2/ Congruency metrics in a CongruencyMetrics.txt file

• Cophenetic correlation with Pearson method
• Cophenetic correlation with Kendall method
• Cophenetic correlation with Spearman method
• Robinson-Foulds distance
• Branch score difference
• Path difference
• Quadratic path difference
• Fowlkes-Mallows index

Illustration

Reference

• First version: Henri C., P. Leekitcharoenphon, H.A. Carleton, N. Radomski, R. S. Kaas, J. F. Mariet, A. Felten, F. M. Aarestrup, P. G. Smidt, S. Roussel, L. Guillier, M.Y. Mistou and R.S. Hendriksen. An assessment of different genomic approaches for inferring phylogeny of Listeria monocytogenes. 2017, Frontiers Microbiology, 8(2351): 1-13, doi.org/10.3389/fmicb.2017.02351
• Second version: Vila Nova M, Durimel K., La K., Felten A., Bessières P., Mistou M.Y., Mariadassou M. and N. Radomski. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. 2019, BMC Genomics, 20(1): 814, doi: 10.1186/s12864-019-6188-x
• Docker Hub: https://hub.docker.com/r/nicolasradomski/treetocongruency

Acknowledgment

My colleague Antonio Rinaldi for our fruitful exchanges about Rscript

Author

Antonio Rinaldi and Nicolas Radomski