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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
accuracy level of co-evolution inference: slow and accurate
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 selected for the projection of phyletic pattern are presented using Archaeopteryx (Han, Zmasek 2009). Here, different genes are represented by columns, in which presence and absence are colored purple, and green, respectively.
    Additionally CoPAP automatically produces phylogenetic visualization of the presence and absence pattern for given pair of genes. Using the FigTree applet, the pattern for a given gene is represented as a tree with taxa names colored according to existence in both ('11', red), absence in both ('00', grey), presence in the first only ('10', green), or presence in the second only ('01', blue).

Co-evolutionary analysis statistics
  • Number of significant interactions = 10181, with FDR of 0.01
  • FDR (BH threshold) for selected p-value of 0.01 = 6.15473e-05
  • Number of tested interaction (pairs of genes with minimal evolution) = 8268211
  • Number of simulated interactions to infer co-evolution (pairs of simulated positions) = 2038037928

  • Duration of estimating evolutionary model parameter = 86.611 hours
  • Duration of mapping events = 174.4 hours
  • Mean duration of co-evolution simulations (per iteration) = 6.166 hours, with 100 iterations.
  • Total running time = 792.133 hours
Underlying evolutionary model used in the analysis