Orthoscape

Orthoscape aimed to analyze evolutionary information in the gene networks and gene sets
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/BioPAX 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]

1.104

Works with Cytoscape 3.0

Release Notes

Fixed PAML inability to work with some KEGG sequences (PAML now works with sequences ended by stop codons)

1.103

Works with Cytoscape 3.0

Release Notes

Some DI bugfixes

1.102

Works with Cytoscape 3.0

Release Notes

Fixed logic error in "online only" mode.

1.101

Works with Cytoscape 3.0

Release Notes

Minor improvements to the interface.

1.1

Works with Cytoscape 3.0

Release Notes

Cytoscape app store uploading test.

CYTOSCAPE 3

Version 1.104

Released 19 Feb 2017

Works with Cytoscape 3.0

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