PB Unroot - mendessoares/BuddySuite GitHub Wiki

--unroot, -ur

Description

When a predefined outgroup is included in a tree, that tree can be 'rooted' to reflect the most basal common ancestor shared among the included taxa. If the basal state cannot be inferred, than trees should be retained in an unrooted state. The unroot function will strip all trees down to their unrooted form.

Example

Input file: rooted_panxA.nwk

(('BOL-PanxαA',(('Cfu-PanxαA','Lla-PanxαA'),('Vpa-PanxαA',('Lcr-PanxαA','Tin-PanxαA')))),'Edu-PanxαA');

Input tree

#### tree_1 ####
            /------------------------------------------------ BOL-PanxαA
            |
/-----------+                                   /------------ Cfu-PanxαA
|           |           /-----------------------+
|           |           |                       \------------ Lla-PanxαA
|           \-----------+
|                       |           /------------------------ Vpa-PanxαA
+                       \-----------+
|                                   |           /------------ Lcr-PanxαA
|                                   \-----------+
|                                               \------------ Tin-PanxαA
|
\------------------------------------------------------------ Edu-PanxαA

Usage example

$: pb rooted_panxA.nwk -ur

Output

[&U] ('BOL-PanxαA':1.0,(('Cfu-PanxαA':1.0,'Lla-PanxαA':1.0):1.0,('Vpa-PanxαA':1.0,('Lcr-PanxαA':1.0,'Tin-PanxαA':1.0):1.0):1.0):1.0,'Edu-PanxαA':2.0):1.0;

Output tree

#### tree_1 ####
/------------------------------------------------------------ BOL-PanxαA
|
|                                            /--------------- Cfu-PanxαA
|              /-----------------------------+
|              |                             \--------------- Lla-PanxαA
|--------------+
+              |              /------------------------------ Vpa-PanxαA
|              \--------------+
|                             |              /--------------- Lcr-PanxαA
|                             \--------------+
|                                            \--------------- Tin-PanxαA
|
\------------------------------------------------------------ Edu-PanxαA