syntenet

Description

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

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Code

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Topics

Depended on by (1)

People

• Fabrício Almeida-Silva author maintainer
• Kristian K Ullrich author
• Yves Van de Peer author
• Tao Zhao author