

[CRV1]  G. Cardona, F. Rossello, G. Valiente. Tripartitions do not always discriminate phylogenetic networks. arXiv:0707.2376v1 [qbio.PE] 
[CRV2]  G. Cardona, F. Rossello, G. Valiente. A Distance Measure for TreeChild Phylogenetic Networks. Preprint. 
[NetGen]  M.M. Morin, and B.M.E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. Bioinformatics 22(2006), 19211923 
[PhyloNet]  PhyloNet: Phylogenetic Networks Toolkit. http://bioinfo.cs.rice.edu/phylonet 
[BSS]  M. Baroni, C. Semple, and M. Steel. Hybrids in Real Time. Syst. Biol. 55(1):4656, 2006 
The rest of the documentation details each of the object methods.
Title : new Usage : my $obj = new Bio::PhyloNetwork(); Function: Creates a new Bio::PhyloNetwork object Returns : Bio::PhyloNetwork Args : none OR eNewick => string OR graph => Graph::Directed object OR edges => reference to an array OR tree => Bio::Tree::Tree object OR mudata => reference to a hash, leaves => reference to an array OR mudata => reference to a hash, numleaves => integerReturns a Bio::PhyloNetwork object, created according to the data given:
new() creates an empty network. new(eNewick => $str) creates the network whose Extended Newick representation (see description above) is the string $str. new(graph => $graph) creates the network with underlying graph given by the Graph::Directed object $graph new(tree => $tree) creates a network as a copy of the Bio::Tree::Tree object in $tree new(mudata => \%mudata, leaves => \@leaves) creates the network by reconstructing it from its mudata stored in \%mudata and with set of leaves in \@leaves. new(mudata => \%mudata, numleaves => $numleaves) creates the network by reconstructing it from its mudata stored in \%mudata and with set of leaves in (l1..l$numleaves).
Title : is_leaf Usage : my $b=$net>is_leaf($u) Function: tests if $u is a leaf in $net Returns : boolean Args : scalar
Title : is_root Usage : my $b=$net>is_root($u) Function: tests if $u is the root of $net Returns : boolean Args : scalar
Title : is_tree_node Usage : my $b=$net>is_tree_node($u) Function: tests if $u is a tree node in $net Returns : boolean Args : scalar
Title : is_hybrid_node Usage : my $b=$net>is_hybrid_node($u) Function: tests if $u is a hybrid node in $net Returns : boolean Args : scalar
Title : is_tree_child Usage : my $b=$net>is_tree_child() Function: tests if $net is a TreeChild phylogenetic network Returns : boolean Args : Bio::PhyloNetwork
Title : nodes Usage : my @nodes=$net>nodes() Function: returns the set of nodes of $net Returns : array Args : none
Title : leaves Usage : my @leaves=$net>leaves() Function: returns the set of leaves of $net Returns : array Args : none
Title : roots Usage : my @roots=$net>roots() Function: returns the set of roots of $net Returns : array Args : none
Title : internal_nodes Usage : my @internal_nodes=$net>internal_nodes() Function: returns the set of internal nodes of $net Returns : array Args : none
Title : tree_nodes Usage : my @tree_nodes=$net>tree_nodes() Function: returns the set of tree nodes of $net Returns : array Args : none
Title : hybrid_nodes Usage : my @hybrid_nodes=$net>hybrid_nodes() Function: returns the set of hybrid nodes of $net Returns : array Args : none
Title : graph Usage : my $graph=$net>graph() Function: returns the underlying graph of $net Returns : Graph::Directed Args : none
Title : edges Usage : my @edges=$net>edges() Function: returns the set of edges of $net Returns : array Args : noneEach element in the array is an anonimous array whose first element is the head of the edge and the second one is the tail.
Title : tree_edges Usage : my @tree_edges=$net>tree_edges() Function: returns the set of tree edges of $net (those whose tail is a tree node) Returns : array Args : none
Title : hybrid_edges Usage : my @hybrid_edges=$net>hybrid_edges() Function: returns the set of hybrid edges of $net (those whose tail is a hybrid node) Returns : array Args : none
Title : explode Usage : my @trees=$net>explode() Function: returns the representation of $net by a set of Bio::Tree:Tree objects Returns : array Args : none
Title : mudata Usage : my %mudata=$net>mudata() Function: returns the representation of $net by its mudata Returns : hash Args : none$net>mudata() returns a hash with keys the nodes of $net and each value is a muVector object holding its muvector.
Title : heights Usage : my %heights=$net>heights() Function: returns the heights of the nodes of $net Returns : hash Args : none$net>heights() returns a hash with keys the nodes of $net and each value is its height.
Title : mu_distance Usage : my $dist=$net1>mu_distance($net2) Function: Computes the mudistance between the networks $net1 and $net2 on the same set of leaves Returns : scalar Args : Bio::PhyloNetwork
Title : mu_distance_generalized Usage : my $dist=$net1>mu_distance($net2) Function: Computes the mudistance between the topological restrictions of networks $net1 and $net2 on its common set of leaves Returns : scalar Args : Bio::PhyloNetwork
Title : tripartitions Usage : my %tripartitions=$net>tripartitions() Function: returns the set of tripartitions of $net Returns : hash Args : none$net>tripartitions() returns a hash with keys the nodes of $net and each value is a string representing the tripartition of the leaves induced by the node. A string BCA... associated with a node u (e.g.) means, the first leaf is in the set B(u), the second one in C(u), the third one in A(u), and so on.
Title : is_time_consistent Usage : my $b=$net>is_time_consistent() Function: tests if $net is (strong) timeconsistent Returns : boolean Args : none
Title : temporal_representation Usage : my %time=$net>temporal_representation() Function: returns a hash containing a temporal representation of $net, or 0 if $net is not timeconsistent Returns : hash Args : none
Title : contract_elementary Usage : my ($contracted,$blocks)=$net>contract_elementary(); Function: Returns the network $contracted, obtained by contracting elementary paths of $net into edges. The reference $blocks points to a hash where, for each node of $contracted, gives the corresponding nodes of $net that have been deleted. Returns : Bio::PhyloNetwork,reference to hash Args : none
Title : optimal_alignment Usage : my ($weight,$alignment,$wgts)=$net>optimal_alignment($net2) Function: returns the total weight of an optimal alignment, the alignment itself, and partial weights between the networks $net1 and $net2 on the same set of leaves. An optional argument allows one to use the Manhattan (default) or the Hamming distance between muvectors. Returns : scalar,reference to hash,reference to hash Args : Bio::PhyloNetwork, metric => string (optional)Supported strings for the metric parameter are ’Manhattan’ or ’Hamming’.
Title : optimal_alignment_generalized Usage : my ($weight,%alignment)=$net>optimal_alignment_generalized($net2) Function: returns the wieght of an optimal alignment, and the alignment itself, between the topological restriction of the networks $net1 and $net2 on the set of common leaves. An optional argument allows one to use the Manhattan (default) or the Hamming distance between muvectors. Returns : scalar,hash Args : Bio::PhyloNetwork, metric => string (optional)Supported strings for the metric parameter are ’Manhattan’ or ’Hamming’.
Title : topological_restriction Usage : my ($netr1,$netr2)=$net1>topological_restriction($net2) Function: returns the topological restriction of $net1 and $net2 on its common set of leaves Returns : Bio::PhyloNetwork, Bio::PhyloNetwork Args : Bio::PhyloNetwork
Title : eNewick Usage : my $str=$net>eNewick() Function: returns the eNewick representation of $net without labeling internal tree nodes Returns : string Args : none
Title : eNewick_full Usage : my $str=$net>eNewick_full() Function: returns the eNewick representation of $net labeling internal tree nodes Returns : string Args : none
Title : display Usage : my $str=$net>display() Function: returns a string containing all the available information on $net Returns : string Args : none
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