For each external node of Tree tree: Cleans up SWISS-PROT
species names: It removes everything (including ) after a potential
"/", "_", "-", "\", ";", ".".
For each node of Tree tree: Extracts the species name
(as SWISS-PROT abbreviation) from the sequence name
(if SWISS-PROT names are used) and writes it to
the species name field if this is empty.
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.
Recalculates and resets parameters of this Tree:
most-branches-per-external-Node, highest and lowest lnL,
longest distance, number of branches, sum of ext Nodes,
deletes data of root Node if this Tree is unrooted.
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.
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.