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During the search, by default, simulated annealing is used (See Salter and Pearl 2001 for details of settings), where the branch lengths and inheritance probabilities are sampled. In this case, through option -po, as a post-processing, users can optimize the branch lengths and inheritance probabilities of the species networks returned by the search. If the dataset is not large and a large a mount of memory is available, users can use option -o to optimize the branch lengths and inheritance probabilities of every proposed network during the search. In this case, simple hill climbing will be used, and only the first 5 operations for network arrangement will be used. If branch lengths of the gene trees are used (option -bl), the latter case will be applied.
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