Library to work with phylogenetic networks aiming at pure performance
extended Newick refers to this format
edgelist refers to a list of pairs of non-negative integers (one pair per line) separated by any positive number of whitespaces where each integer is smaller than the total number of integers used
For each example x, x -h or x --help will give usage information.
iso is a network isomorphism checker. Invoke iso [-v] <file1> [file2] where either file1 describes 2 networks (in extended Newick, 1 per line), or file1 and file2 both describe a network (either in extended Newick or as an edgelist); -v shows a representation of the two Newick trees.
tc is a tree-containment checker. Invoke tc [-v] <file1> [file2] where either file1 describes a network and a tree (both in extended Newick, 1 per line), or one of file1 and file2 describes a network and the other a tree (either in extended Newick or as an edgelist); -v shows a representation of the two Newick trees.
gen is a generator for binary phylogenetic networks. Invoke gen [-v] [-n <num nodes>] [-r <num reticulations>] [-l <num leaves>] [file]
to write a random network with <num nodes> nodes (num reticulations and num leaves of them being reticulations and leaves, respectively) to file (or standard out if omitted) in extended Newick format. -v shows a representation of the network.
sw can compute a minimum-width extension tree for the input network. See this publication for preliminaries.