What follows is a step-by-step outline of the network construction and analysis methods performed in Mathematica. Each section corresponds to each of the logical tasks carried out to construct and analyze the different network models. Sections are structured in three parts:
All notebooks can be viewed with the free Mathematica Player. Alternatively Mathematica Player Pro or Mathematica
may also be used.01 - Excel data import.nb (Download Mathematica Player to open notebooks)
This notebook imports the data provided in Additional File 3 (sheets AF3A and AF3D) into Mathematica.
02 -
Distributions-Markers bimultigraphs.nb
(Mathematica Player or above required)
Builds and displays bimultigraphs which relate the different states of three polymorphic amino acid motifs (PAMs) present in retroelements with their host distributions.
03 -
Branches-Markers bimultigraphs.nb
(Mathematica Player or above required)
Builds and displays bimultigraphs which relate the different states of three polymorphic amino acid motifs (PAMs) present in retroelement lineages with their branch groups.
04a - MCs
feature vectors builder.nb
04b - Phenotypic neighbors network.nb
(Mathematica Player or above required)
Creates a list of non-redundant feature vectors from 8 PAMs and constructs a network on the basis of vector distances considering trait changes as edges (linking phenotypic neighbors). This network is presented as a multigraph taking all lineage changes between two MCs as multiple edges.
05a - Phenotypic neighbors network analysis.nb
05b - Phenotypic neighbors network analysis (lineage multiedges).nb
(Mathematica Player or above required)
The networks in the previous section are transformed into adjacency matrices and their degree distribution, average clustering coefficient and mean shortest path length are calculated.