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Running Parameters:

Job title: Toy example
Presence-Absence = Presence-Absence Data
Tree = Tree
Genes annotation file = Genes annotation file

Co-evolution computation
co-evolutionary interactions p-value: 0.01
accuracy level of co-evolution inference: normal speed and accuracy

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
Co-evolutionary analysis statistics
  • Number of significant interactions = 19, with FDR of 0.01
  • FDR (BH threshold) for selected p-value of 0.01 = 0.000856757
  • Number of tested interaction (pairs of genes with minimal evolution) = 105
  • Number of simulated interactions to infer co-evolution (pairs of simulated positions) = 45255716

  • Duration of estimating evolutionary model parameter = 0.000 minutes
  • Duration of mapping events = 0.017 minutes
  • Mean duration of co-evolution simulations (per iteration) = 0.857 minutes, with 10 iterations.
  • Total running time = 8.567 minutes
Underlying evolutionary model used in the analysis