Orthoscape is a Cytoscape application aimed to perform evolutionary analysis of gene networks and visualize the results.
Orthoscape can perform the following actions either for a gene network/metabolic pathway or simple set of genes:
1) Calculate evolutionary indices for every gene and analyze distributions of these indices in a network:
a) Phylostratigraphic Age Index (PAI). PAI indicates the evolutionary age of a gene by searching the last common ancestor for a species representing the original gene and every species representing the orthologous genes;
b) Divergency index (DI). DI reflects the influence of natural selection on gene evolution. It is based on Ka/Ks (dN/dS) ratio between gene and every ortholog. To calculate Ka/Ks we use KaKs Calcultor and PAML.
2) Group genes into clusters according to their homology level calculated using
a) Nucleotide sequences identity value;
b) Smith-Waterman's algorithm score;
c) Similarity of protein domains.
3) Rearrange/layout/color gene networks and metabolic pathways according to evolutionary indices PAI and DI as well as homology groups.
The Orthoscape input is either data from KEGG/Pathway Commons pathway databases or result from network reconstruction plugin GeneMANIA.
More information in the paper: [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1427-5 Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles]