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Running Parameters:

Presence-Absence = Presence-Absence Data
Tree = Tree
Genes annotation file = Genes annotation file

Co-evolution computation
co-evolutionary interactions p-value: 0.01
number of simulated iterations: 100
minimal number of events required in characters to look for co-evolution: 4

Evolutionary model
gain & loss rates: Variable rate among sites
Rate Distribution Type: Gamma plus invariant category
Correction for un-observable data
Minimum number of Ones: 1
Minimum number of Zeros: 0
Estimation of model parameters
Estimate all model parameters using likelihood: Yes
Estimate branch lengths using likelihood: No
Optimization Level: Medium
Number of Categories: 3


Visualize co-evolutionary network using Cytoscape
Global properties of the network
Position-specific projection of pattern onto the phylogeny
  • Project position
    presence onto phylogeny (you can select multiple positions by holding ctrl while selecting)
    Positions-specific patterns are projected by coloring the taxa according to presence (red) absence (blue).
    Additionally, for the set of selected position for comparison (e.g., x,y,z), taxa in which the character is present uniquely in position x (absent in these taxa for y,z) are colored in green.

Co-evolutionary analysis statistics
  • Number of simulated interactions = 2038037928
  • FDR (BH threshold) for selected p-value = 6.15473e-05
  • Number of significant interactions = 10181
  • Number of tested interaction (pairs of genes with minimal evolution) = 8268211
Underlying evolutionary model used in the analysis