Usage

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

Dependencies

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

• library(ape)
• library(ggplot2)
• library(maps)
• library(phytools)
• library(viridis)
• library(dplyr)
• library(phylogram)
• library(phangorn)
• library(dendextend)

Install R from configured sources (Ubuntu 20.04)

sudo apt update
sudo apt install r-base
R --version

Update R

1/ Check the current R version

R --version

2/ Update and upgrade apt-get

sudo apt-get update
sudo apt-get upgrade

3/ Check the available lastest R version

sudo apt-cache showpkg r-base

4/ Update the lastest R version

sudo apt-get install r-base

5/ Check the updated R version

R --version

Install dependencies and launch the R script

1/ Unpack the GitHub repository and move inside

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

2/ Install dependencies

R
install.packages("ape")
install.packages("ggplot2")
install.packages("maps")
install.packages("phytools")
install.packages("viridis")
install.packages("dplyr")
install.packages("phylogram")
install.packages("phangorn")
install.packages("dendextend")
quit()

3/ Launch the R script

Rscript TreeToCongruency.R tree1.nwk tree2.nwk

Expected output files

• figures of pairwise trees (tanglegram.pdf and tanglegram.tiff)
• estimation of the Robinson-Foulds distance (RF.txt)
• estimation of the Robinson-Foulds indexes (FM-indexes.txt)
• estimation of the Fowlkes-Mallows indexes (RF-indexes.txt)
• estimate the Cophenetic correlations (CC-kendall.txt, CC-person.txt and CC-spearman.txt)

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

Acknowledgment

My colleague Antonio Rinaldi for our fruitful exchanges about Rscript

Author

Nicolas Radomski email: n.radomski@izs.it