Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
use Bio::TreeIO; my $in = new Bio::TreeIO(-format => 'newick', -file => 'tree.tre'); my $tree = $in->next_tree; my @nodes = $tree->find_node('id1'); if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){ #... }
This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.
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Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.edu
Sendu Bala, bix@sendu.me.uk
Rerooting code was worked on by
Daniel Barker d.barker-at-reading.ac.uk Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : find_node Usage : my @nodes = $self->find_node(-id => 'node1'); Function: returns all nodes that match a specific field, by default this is id, but different branch_length, Returns : List of nodes which matched search Args : text string to search for OR -fieldname => $textstring
Title : remove_Node Usage : $tree->remove_Node($node) Function: Removes a node from the tree Returns : boolean represent status of success Args : either Bio::Tree::NodeI or string of the node id
Title : get_lineage_nodes Usage : my @nodes = $tree->get_lineage_nodes($node); Function: Get the full lineage of a node (all its ancestors, in the order root->most recent ancestor) Returns : list of nodes Args : either Bio::Tree::NodeI or string of the node id
Title : splice Usage : $tree->splice(-remove_id => \@ids); Function: Remove all the nodes from a tree that correspond to the supplied args, making all the descendents of a removed node the descendents of the removed node's ancestor. You can ask to explicitly remove certain nodes by using -remove_*, remove them conditionally by using -remove_* in combination with -keep_*, or remove everything except certain nodes by using only -keep_*. Returns : n/a Args : just a list of Bio::Tree::NodeI objects to remove, OR -key => value pairs, where -key has the prefix 'remove' or 'keep', followed by an underscore, followed by a fieldname (like for the method find_node). Value should be a scalar or an array ref of scalars (again, like you might supply to find_node). So (-remove_id => [1, 2]) will remove all nodes from the tree that have an id() of '1' or '2', while (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with an id() of '1'. (-keep_id => [2]) will remove all nodes unless they have an id() of '2' (note, no -remove_*).
Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no commen ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes
Title : merge_lineage Usage : merge_lineage($node) Function: Merge a lineage of nodes with this tree. Returns : n/a Args : Bio::Tree::TreeI with only one leaf, OR Bio::Tree::NodeI which has an ancestor For example, if we are the tree $tree: +---B | A | +---C and we want to merge the lineage $other_tree: A---C---D After calling $tree->merge_lineage($other_tree), $tree looks like: +---B | A | +---C---D
Title : contract_linear_paths Usage : contract_linear_paths() Function: Splices out all nodes in the tree that have an ancestor and only one descendent. Returns : n/a Args : none For example, if we are the tree $tree: +---E | A---B---C---D | +---F After calling $tree->contract_linear_paths(), $tree looks like: +---E | A---D | +---F
Title : distance Usage : distance(-nodes => \@nodes ) Function: returns the distance between two given nodes Returns : numerical distance Args : -nodes => arrayref of nodes to test
Title : is_monophyletic Usage : if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outgroup) Function: Will do a test of monophyly for the nodes specified in comparison to a chosen outgroup Returns : boolean Args : -nodes => arrayref of nodes to test -outgroup => outgroup to serve as a reference
Title : is_paraphyletic Usage : if( $tree->is_paraphyletic(-nodes =>\@nodes, -outgroup => $node) ){ } Function: Tests whether or not a given set of nodes are paraphyletic (representing the full clade) given an outgroup Returns : [-1,0,1] , -1 if the group is not monophyletic 0 if the group is not paraphyletic 1 if the group is paraphyletic Args : -nodes => Array of Bio::Tree::NodeI objects which are in the tree -outgroup => a Bio::Tree::NodeI to compare the nodes to
Title : reroot Usage : $tree->reroot($node); Function: Reroots a tree making a new node the root Returns : 1 on success, 0 on failure Args : Bio::Tree::NodeI that is in the tree, but is not the current root
Title : findnode_by_id Usage : my $node = $tree->find_node_by_id($id); Function: Get a node by its internal id (which should be unique for the tree) Returns : L<Bio::Tree::NodeI> Args : node id
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.