CPNetwork

CPNetwork: a pipeline to plot Network software results in a custom way

The Network software (https://www.fluxus-engineering.com/sharenet.htm) is a free phylogenetic network software that generates evolutionary trees and networks from genetic, linguistic, and other data.

Sometimes, in particular with complex datasets, the graphical output of the obtained networks is difficult to resolve, with overlapping edges or crowded nodes, and the network customization is tricky.

For these reasons, we are proposing a pipeline to plot Network software results in a highly customizable way called CPNetwork (Custom Plot Network).

Materials in the repository

In the repository are present:

• CustomPlotNetwork_Manual.pdf: manual of CPNetwork pipeline
• SCRIPT/CPNetwork_parseFDI.py: to parse the .fdi file from Network software to extract information on nodes, edges and equivalent taxa files
• SCRIPT/CPNetwork_[*]Network.R: R scripts to plot a Custom Plot Network, with piechart (CPNetwork_pieNetwork.R) or without piechart (CPNetwork_plotNetwork.R)
• EXAMPLE/Network: example .fdi file from Network software. Output from CPNetwork_parseFDI.py and CPNetwork_plotNetwork.R are reported
• EXAMPLE/Custom: example .fdi file used in Migliore et al. (2025) paper. Output from CPNetwork_parseFDI.py are reported

How the pipeline works

The .fdi file, the final output file from Network software, is firstly parsed with a Python script to extract information on nodes, edges and equivalent taxa files. Secondly, the files containing the extracted information are used in an R script to plot the custom network.

Parsing

The CPNetwork_parseFDI.py script is a Python script (version >3) created to parse the .fdi file from Network software.

Custom plot

The CPNetwork_pieNetwork.R and CPNetwork_plotNetwork.R scripts are R scripts created to plot a custom network. In the first case, pie charts are used to represent the OUT. The Igraph R package (version >= 1.1.2) [72] is used.

How to cite

Rambaldi Migliore, N.; Bigi, D.; Milanesi, M.; Zambonelli, P.; Negrini, R.; Morabito, S.; Verini-Supplizi, A.; Liotta, L.; Chegdani, F.; Agha, S.; et al. Mitochondrial DNA Control-Region and Coding-Region Data Highlight Geographically Structured Diversity and Post-Domestication Population Dynamics in Worldwide Donkeys. PLoS ONE 2024, 19, e0307511, doi:10.1371/journal.pone.0307511.

Maintainers contacts

• Marco Milanesi marco.milanesi.mm@gmail.com