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bioRxiv · 10.1101/2022.08.16.504079

syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

Almeida-Silva, F.·Zhao, T.·Ullrich, K. K.·Van de Peer, Y.
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Abstract

Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate. Availability and ImplementationThe package is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).

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Almeida-Silva, F., Zhao, T., Ullrich, K. K., Van de Peer, Y.. 2022-08-16. syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. https://doi.org/10.1101/2022.08.16.504079

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