PhyloNetworks: estimate & plot phylogenetic networks
goal: use data in the form of gene trees or quartet concordance factors, to estimate a phylogenetic network: for species relationships that may include gene flow or hybridization
- Introduction: explicit networks, introduction to Julia and simple functions in PhyloNetworks: read/write/plot/root networks.
- SNaQ: maximum pseudolikelihood estimation of networks.
- Choice of number of hybridizations
- Bootstrap analysis
In the folder data_results, there are different datasets. We will use the dataset baseline.gamma0.3_n30.
The script that we will follow is called tutorial.jl and it is in scripts.
