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The evolutionary relationships between sequences were also reconstructed using the package Network [ 52].
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All calculations were done in R using the package qpgraph and networks were visualized using Cytoscape (www.cytoscape.org) and yEd (www.yworks.com) graphical editors.
Anatomical networks were coded as adjacency matrices in Excel sheets and analyzed in R49 using the package igraph 50.
A median joining network (Bandelt et al. 1995) was constructed using the Network 4.5.0.0 package (http://www.fluxus-engineering.com/) for each of the four main haplogroups (A2, B2, C1, and D1) found in Mexican populations.
Simulation of this system is achieved using the network simulation package (NS2).
In this section, a simulation environment is constructed using the network simulation package (NS2) [57].
Gene networks were constructed with the MetaCore package using the algorithms "network analysis" and "receptor targets modeling".
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