Among them, Cytoscape is one of the most comprehensive tools for performing all-round analysis of biological networks. There are software packages to work with biological networks with less or more biological specialization, availability and interactivity. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.īiological networks arise in completely all fields of modern biology gathering both ‘real’ (experimental data etc.) and virtual (modeling and simulation data) biological information. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes (2) the evolutionary origin of gene network components (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Nevertheless, only three plugins tagged ‘network evolution’ found in Cytoscape official app store and in literature. Among them, Cytoscape ( ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. There are many available software tools for visualization and analysis of biological networks.
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