These user-specified parameters are explained below: In it, we have to specify the parameters needed to automate the process. Eventually, the control panel illustrated on the second image of the screenshots section will appear. Once selected (the network must be shaded), you can execute the application by selecting the option “Proceed” in Apps > Inbreeding of the upper menu.
#CYTOSCAPE DIRECTED GRAPH INSTALL#
Eventually, it will show the app and you can finally install it by clicking on “Install”.Īfter installing the Inbreeding app and loading the network containing the parental relationships among individuals, the next step (prior to the execution of the app) is to select the loaded network by clicking on it. After that, you just need to search the app by typing the name “Inbreeding” in the search bar. Once done, you can install the Inbreeding app by navigating to the upper menu of the environment and clicking on Apps > AppManager. As an example of this, we can see the first image of the screenshots section.įor the installation of the app, you need to first configure your own Cytoscape 3.x environment downloading it from. As expected, a child node can only have 2 or less parent nodes (two edges pointing him/her) representing the mother and/or father relationship. In this sense, edges leaving a node indicate that this node is parent of the node to which the edge points. The needed network is a directed graph where the nodes identify each distinct individual by a unique name and the edges between them determine their parental relationships. Therefore, prior to the execution of this application, the user, in any way he/she wants, must have loaded a network (mating network) containing all this information. At the end, Inbreeding exports the result (inbreeding and relationship coefficients among all the individuals) into a csv file format for posterior easy viewing.Īs stated above, this app uses information on parental relationships of individuals to calculate their inbreeding and relatedness coefficients. In order to automate this process, a network with the parental relationships of the individuals (mating network) must be provided. The Cytoscape 3.* app Inbreeding, given a mating network, calculates the inbreeding and relationship/relatedness coefficients between the individuals composing the input network.
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