PB Collapse polytomies

--collapse_polytomies, -cpt

Description

Remove nodes if their support value or branch length are below a given threshold

Argument

Threshold (float).

Optional. Set the minimum support or length of a node or edge (respectively) for it to be retained. The default is '50', which may not be very appropriate for you tree.

Mode ({'support'|'length'})

Optional. Specify whether branch length or support values are used to determine whether a node is collapsed. Default is 'support'.

Examples

input file: Mle-Panx.nwk

Note the format used here for bootstrap support is square brackets following a branch length. This is not the standard format PhyloBuddy uses, and while readable, the output will be returned as 'support:branch length'.

(Mle-Panxα4:1.0368,(Mle-Panxα9:0.4979,(((Mle-Panxα2:1.1345,(Mle-Panxα1:1.7479,Mle-Panxα5:0.9697):0.1782[80]):0.0857[100],Mle-Panxα6:0.5312):0.0433[35],Mle-Panxα8:0.8720):0.0941[48]):0.0643[90],Mle-Panxα3:0.8686);

Usage example 1

Default settings

$: pb Mle-Panx.nwk -cpt

output

('Mle-Panxα4':1.0368,('Mle-Panxα9':0.4979,'Mle-Panxα8':0.872,('Mle-Panxα2':1.1345,('Mle-Panxα1':1.7479,'Mle-Panxα5':0.9697)80:0.1782)100:0.0857,'Mle-Panxα6':0.5312)90:0.0643,'Mle-Panxα3':0.8686);

Usage example 2

Branch lengths are used in this example, but be aware that only branched on internal nodes will be modified (i.e., not branched leading to tips).

$: pb Mle-Panx.nwk -cpt length 0.1

output

('Mle-Panxα4':1.0368,'Mle-Panxα3':0.8686,'Mle-Panxα9':0.4979,'Mle-Panxα8':0.872,'Mle-Panxα6':0.5312,'Mle-Panxα2':1.1345,('Mle-Panxα1':1.7479,'Mle-Panxα5':0.9697)80:0.1782);