For each external node of Tree tree: Cleans up SWISS-PROT
species names: It removes everything (including ) after a potential
"/", "_", "-", "\", ";", ".".
This method is mainly to be used by the RIO classes as the returned tree
is quite incomplete -- for improved time efficiency (number of external
nodes of each Node are off, will have lost most annotations).
Traverses the subtree of Node g in postorder, calculating the
mapping function M, and determines which nodes
represent speciation events and which ones duplication
events.
Calculates the distance of the Node with seq name seq_name
to the LCA of ext_nodes, which has been set either with
constructor DistanceCalculator(Tree,Vector) or method
setTreeAndExtNodes(Tree,Vector).
Calculates the distance of Node n to the root of Tree t which
has been set either with a constructor, setTree(Tree), or
setTreeAndExtNodes(Tree,Vector).
Calculates the distance of the Node with seq name seq_name
to the root of Tree t, which has been set either with a
constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector).
Returns the (absolue value of the) minimal difference in tree heights
of the two subtrees at the root (of the (re)rooted gene tree)
- as determined by method "infer" - if minimize_height is set to true.
Returns the order in which ortholog (o),
"super ortholog" (s) and distance (d) are
returned and sorted (priority of sort always
goes from left to right), given sort.
Infers for each Node of gene_tree (set in constructor) whether it
represents a speciation or duplication event by calculating
and interpreting the mapping function M.
Infers for each Node of gene_tree (set in constructor) whether it
represents a speciation or duplication event by calculating
and interpreting the mapping function M.
Infers for each Node of gene_tree (set in constructor) whether it
represents a speciation or duplication event by calculating
and interpreting the mapping function M.
Infers the orthologs (and "super orthologs") for each external node
of the gene Trees in multiple tree File gene_trees_file
(=output of PHYLIP NEIGHBOR, for example).
Infers the orthologs (and "super orthologs") for each external node
of the gene Trees in multiple tree File gene_trees_file
(=output of PHYLIP NEIGHBOR, for example).
Calculates the mapping function for the external nodes of the gene
tree: links (sets the field "link" of Node) each external Node of gene_tree
to the external Node of species_tree which has the same species name.
Arranges the order of childern for each node of this Tree in such
a way that either the branch with more children is on top (right)
or on bottom (left), dependent on the value of boolean order.
Reads in multiple Trees from a File multipletreefile,
containing Tree descriptions in New Hampshire (NH) or
New Hampshire X (NHX) format separated by semicolons followed
by a newline.
Sets a boolean which could represent whether placement
of an additional Node on the parent branch of this Node
makes the likelihood of the resulting tree significantly worse.
Sets the rooted Tree t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance
and standard deviation are calculated.
Sets the rooted Tree t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance
and standard deviation are calculated.
Returns a boolean which could represent whether placement
of an additional Node on the parent branch of this Node
makes the likelihood of the resulting tree significantly worse.