PB Add branch

--add_branch, -ab

Description

Place a new branch into a tree (either a single tip or subtree)

Argument

branch/subtree (str or path).

Specify a taxon name, or entire subtree in a supported format, to be added to the input tree.

sister [sister ...] (regex)

Specify where the new subtree should be appended. Note that the values passed in will be interpreted as regular expressions and partial matches will be included. If you want a specific taxon with a name that is a subset of other taxa names, use the following:

"^taxon_id_001$".

Now, 'pig_taxon_id_0011' will not be matched.

Examples

input file: Mle-Panx.nwk

(Mle-Panxα4:1.03,(Mle-Panxα9:0.49,(((Mle-Panxα2:1.13,(Mle-Panxα1:1.74,Mle-Panxα5:0.96):0.17):0.08,Mle-Panxα6:0.53):0.04,Mle-Panxα8:0.87):0.09):0.06,Mle-Panxα3:0.86);

Usage example 1

Single taxon added sister to a single taxon

$: pb Mle-Panx.nwk -ab "Hech-Panxβ" "^Mle-Panxα1$"

output

('Mle-Panxα4':1.03,('Mle-Panxα9':0.49,((('Mle-Panxα2':1.13,('Mle-Panxα5':0.96,('Hech-Panxβ':0.87,'Mle-Panxα1':0.87):0.87):0.17):0.08,'Mle-Panxα6':0.53):0.04,'Mle-Panxα8':0.87):0.09):0.06,'Mle-Panxα3':0.86);

Usage example 2

Subtree added sister to a single taxon

$: pb Mle-Panx.nwk -ab "((Hech-Panxβ1,Hech-Panxβ2),Hech-Panxβ3);" "α8"

output

('Mle-Panxα4':1.03,('Mle-Panxα9':0.49,((('Mle-Panxα2':1.13,('Mle-Panxα1':1.74,'Mle-Panxα5':0.96):0.17):0.08,'Mle-Panxα6':0.53):0.04,((('Hech-Panxβ1':1.0,'Hech-Panxβ2':1.0):1.0,'Hech-Panxβ3':1.0):0.435,'Mle-Panxα8':0.435):0.435):0.09):0.06,'Mle-Panxα3':0.86);

Usage example 3

Subtree in a file added sister to a clade with multiple taxa

$: pb Mle-Panx.nwk -ab "/path/to/Hech_tree.nex" "α2" "α5"

output

('Mle-Panxα4':1.03,('Mle-Panxα9':0.49,(('Mle-Panxα6':0.53,(('Mle-Panxα2':1.13,('Mle-Panxα1':1.74,'Mle-Panxα5':0.96):0.17):0.04,(('Hech-Panxβ1':1.0,'Hech-Panxβ2':1.0):1.0,'Hech-Panxβ3':1.0):0.04):0.04):0.04,'Mle-Panxα8':0.87):0.09):0.06,'Mle-Panxα3':0.86);