syntenet-package: syntenet: Inference And Analysis Of Synteny Networks

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

syntenet: Inference And Analysis Of Synteny Networks

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.

Author(s)

Maintainer: Fabrício Almeida-Silva [e-mail] (ORCID)

Authors:

• Tao Zhao [e-mail] (ORCID)

• Kristian K Ullrich [e-mail] (ORCID)

• Yves Van de Peer [e-mail] (ORCID)

See Also

Useful links:

• https://github.com/almeidasilvaf/syntenet

• Report bugs at https://support.bioconductor.org/t/syntenet

almeidasilvaf/syntenet documentation built on Oct. 12, 2024, 5:51 p.m.