PhyloNetwork documentation.

 use Bio::PhyloNetwork;

 # Create a PhyloNetwork object from a eNewick string
 my $net1=Bio::PhyloNetwork->new(
   -eNewick=>'t0:((H1,(H2,l2)),H2); H1:((H3,l1)); H2:((H3,(l3,H1))); H3:(l4);'
 );

 # Print all available data
 print $net1;

 # Rebuild $net1 from its mu_data
 my %mudata=$net1->mudata();
 my $net2=Bio::PhyloNetwork->new(-mudata=>\%mudata,-numleaves=>4);
 print $net2;
 print "d=".$net1->mu_distance($net2)."\n";

 # Get another one and compute distance
 my $net3=Bio::PhyloNetwork->new(
   -eNewick=>'(l2,((l1,(H1,l4)),H1))r; (l3)H1;'
 );
 print "d=".$net1->mu_distance($net3)."\n";

 # ...and find an optimal alignment w.r.t. the Manhattan distance (default)
 my ($weight,%alignment)=$net1->optimal_alignment($net3);
 print "weight:$weight\n";
 foreach my $node1 (keys %alignment) {
   print "$node1 => ".$alignment{$node1}."\n";
 }
 # ...or the Hamming distance

 my ($weightH,%alignmentH)=$net1->optimal_alignment($net3,-metric=>'Hamming');
 print "weight:$weightH\n";
 foreach my $node1 (keys %alignmentH) {
   print "$node1 => ".$alignmentH{$node1}."\n";
 }

 # Test for time consistency of $net1
 if ($net1->is_time_consistent) {
   print "net1 is time consistent\n"
 }
 else {
   print "net1 is not time consistent\n"
 }

 # create a network from the list of edges
 my $net4=Bio::PhyloNetwork->new(-edges=>
   [qw(r s r t s u s c t c t v u b u l3 u b v b v l4 b l2 c l1)]);

 # Test for time consistency of $net3
 if ($net4->is_time_consistent) {
   print "net4 is time consistent\n"
 }
 else {
   print "net4 is not time consistent\n"
 }

 # And print all information on net4
 print $net4;

 # Compute some tripartitions
 my %triparts=$net1->tripartitions();

 # Now these are stored
 print $net1;

 # And can compute the tripartition error
 print "dtr=".$net1->tripartition_error($net3)."\n";

Description

This is a module to work with phylogenetic networks. Phylogenetic networks
have been studied over the last years as a richer model of the evolutionary
history of sets of organisms than phylogenetic trees, because they take not
only mutation events but also recombination and horizontal gene transfer
events into account.
The natural model for describing the evolutionary
history of a set of sequences under recombination events is a DAG, hence
this package relies on the package Graph::Directed to represent the
underlying graph of a phylogenetic network. We refer the reader to [CRV1,CRV2]
for formal definitions related to phylogenetic networks. With this package, phylogenetic networks can be given by its eNewick
string. This description appeared in other packages related to
phylogenetic networks (see [PhyloNet] and [NetGen]); in fact, these two
packages use different descriptions. The Bio::PhyloNetwork
package allows both of them, but uses the second one in its output.
The first approach [PhyloNet] goes as follows: For each hybrid node H, say with
parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k+1 different
nodes; let each of the first k copies be a child of one of the u_1,...,u_k
(one for each) and have no children (hence we will have k extra leaves);
as for the last copy, let it have no parents and have v_1,...,v_l be its
children. This way we get a forest; each of the trees will be rooted at either
one root of the phylogenetic network or a hybrid node of it; the set of leaves
(of the whole forest) will be the set of leaves of the original network
together with the set of hybrid nodes (each of them repeated as many times
as its in-degree). Then, the eNewick representation of the phylogenetic network
will be the Newick representation of all the trees in the obtained forest,
each of them with its root labeled.
The second approach [NetGen] goes as follows: For each hybrid node H, say with
parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k different
nodes; let the first copy be a child of u_1 and have all v_1,v_2,...v_l as
its children; let the other copies be child of u_2,...,u_k (one for each)
and have no children. This way, we get a tree whose set of leaves is the
set of leaves of the original network together with the set of hybrid nodes
(possibly repeated). Then the Newick string of the obtained tree (note that
some internal nodes will be labeled and some leaves will be repeated) is
the eNewick string of the phylogenetic network.
For example, consider the network depicted below:

       r
      / \
     /   \
    U     V
   / \   / \
  1   \ /   3
       H
       |
       2

If the first approach is taken, we get the forest:

       r
      / \
     /   \
    U     V
   / \   / \
  1   H H   3
       |
       H
       |
       2

Hence, the eNewick string is '((1,H),(H,3))r; (2)H;'.
As for the second one, one gets the tree:

       r
      / \
     /   \
    U     V
   / \   / \
  1   H |   3
        H
        |
        2

Hence, the eNewick string is '((1,H),((2)H,3))r;'.
Note: when rooting a tree, this package allows the notations
'(subtree,subtree,...)root' as well as 'root:(subtree,subtree,...)', but
the first one is used when writing eNewick strings. Tree-child (TC) phylogenetic networks are a special class of phylogenetic
networks for which a distance, called mu-distance, is defined [CRV2]
based on certain data (mu-data) associated to every node.
Moreover, this distance extends the
Robinson-Foulds on phylogenetic trees. This package allows testing for a
phylogenetic network if it is TC and computes mu-distances between networks
over the same set of leaves.
Moreover, the mu-data allows one to define the optimal
(in some precise sense) alignment between networks
over the same set of leaves. This package also computes this optimal alignment. Although tripartitions (see [CRV1] and the references therein) do not allow
to define distances, this package outputs tripartitions and computes a weak
form of the tripartition error. Another useful property of Phylogenetic Networks that appears in the literature
is that of time-consistency or real-time hybrids [BSS]. Roughly speaking, a
network admits a temporal representation if it can be drawn in such a way
that tree arcs (those whose end is a tree node) are inclined downwards, while
hybridization arcs (those whose end is a hybrid node) are horizontal.
This package checks for time-consistency and, if so, a temporal representation
is provided.

Methods

new	Description	Code
build_from_edges	No description	Code
build_from_graph	No description	Code
build_from_eNewick	No description	Code
process_block	No description	Code
get_root_and_subtree	No description	Code
get_label_type_id_length	No description	Code
trim	No description	Code
my_split	No description	Code
build_from_mudata	No description	Code
build_from_tree	No description	Code
recompute	No description	Code
is_attackable	No description	Code
do_attack	No description	Code
compute_mu	No description	Code
compute_height	No description	Code
is_leaf	Description	Code
is_root	Description	Code
is_tree_node	Description	Code
is_hybrid_node	Description	Code
has_tree_child	No description	Code
is_tree_child	Description	Code
nodes	Description	Code
leaves	Description	Code
roots	Description	Code
internal_nodes	Description	Code
tree_nodes	Description	Code
hybrid_nodes	Description	Code
graph	Description	Code
edges	Description	Code
tree_edges	Description	Code
hybrid_edges	Description	Code
explode	Description	Code
explode_rec	No description	Code
mudata	Description	Code
mudata_node	No description	Code
heights	Description	Code
height_node	No description	Code
mu_distance	Description	Code
mu_distance_generalized	Description	Code
mudata_string_node	No description	Code
mudata_string	No description	Code
is_mu_isomorphic	No description	Code
compute_tripartition_node	No description	Code
compute_tripartitions	No description	Code
tripartitions	Description	Code
tripartition_error	No description	Code
is_time_consistent	Description	Code
temporal_representation	Description	Code
compute_temporal_representation	No description	Code
find_classes	No description	Code
join_classes	No description	Code
contract_elementary	Description	Code
optimal_alignment	Description	Code
optimal_alignment_noelementary	No description	Code
optimal_alignment_generalized	Description	Code
weight	No description	Code
topological_restriction	Description	Code
eNewick	Description	Code
eNewick_aux	No description	Code
make_label	No description	Code
eNewick_full	Description	Code
eNewick_full_aux	No description	Code
make_label_full	No description	Code
display	Description	Code

Methods description

new