Package ete2 :: Package phylo :: Module spoverlap
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Module spoverlap

source code

Functions [hide private]
 
get_evol_events_from_leaf(node, sos_thr=0.0)
Returns a list of duplication and speciation events in which the current node has been involved.
source code
 
get_evol_events_from_root(node, sos_thr)
Returns a list of **all** duplication and speciation events detected after this node.
source code
Variables [hide private]
  __VERSION__ = 'ete2-2.0rev104'
  __package__ = 'ete2.phylo'
Function Details [hide private]

get_evol_events_from_leaf(node, sos_thr=0.0)

source code 

Returns a list of duplication and speciation events in which the current node has been involved. Scanned nodes are also labeled internally as dup=True|False. You can access this labels using the 'node.dup' sintaxis.

Method: the algorithm scans all nodes from the given leafName to the root. Nodes are assumed to be duplications when a species overlap is found between its child linages. Method is described more detail in:

"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. Genome Biol. 2007;8(6):R109.

get_evol_events_from_root(node, sos_thr)

source code 

Returns a list of **all** duplication and speciation events detected after this node. Nodes are assumed to be duplications when a species overlap is found between its child linages. Method is described more detail in:

"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon T. Genome Biol. 2007;8(6):R109.