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--root, -rt
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 root function will root/re-root a tree at its midpoint or at specified nodes.
Arguments
Taxa label(s) ( str )
Optional. One or more taxa labels can be used to place the root.
- 0 labels: The tree is rooted at the node which represents the most recent common ancestor between the two most divergent taxa in the tree.
- 1 label: The tree is rooted on the taxa provided
- 2+ labels: The tree is rooted on the node which represents the most recent common ancestor shared by all included taxa
Note: Labels must match exactly (case sensitive), otherwise the root method will default to midpoint.
Examples
Input file: unrooted_panxA.nwk
('BOL-PanxαA':0.23575,'Edu-PanxαA':0.38304,(('Cfu-PanxαA':0.51865,'Lla-PanxαA':0.25913)0.994:0.2571,('Vpa-PanxαA':0.87256,('Lcr-PanxαA':0.77097,'Tin-PanxαA':0.81535)0.972:0.27115)0.851:0.14015)0.190:0.10821);
Input tree
#### tree_1 ####
/-------------------------------------------------------------------- BOL-PanxαA
|
|-------------------------------------------------------------------- Edu-PanxαA
+
| /----------------- Cfu-PanxαA
| /---------------------------------+
| | \----------------- Lla-PanxαA
\----------------+
| /---------------------------------- Vpa-PanxαA
\----------------+
| /----------------- Lcr-PanxαA
\----------------+
\----------------- Tin-PanxαA
Usage example 1
$: pb unrooted_panxA.nwk -rt
Output
[&R] (('Lcr-PanxαA':0.77097,'Tin-PanxαA':0.81535)0.972:0.27115,'Vpa-PanxαA':0.87256,(('Cfu-PanxαA':0.51865,'Lla-PanxαA':0.25913)0.994:0.2571,('BOL-PanxαA':0.23575,'Edu-PanxαA':0.38304):0.10821)0.190:0.14015);
Output tree
#### tree_1 ####
/---------------------- Lcr-PanxαA
/---------------------------------------------+
| \---------------------- Tin-PanxαA
|
|-------------------------------------------------------------------- Vpa-PanxαA
+
| /---------------------- Cfu-PanxαA
| /----------------------+
| | \---------------------- Lla-PanxαA
\----------------------+
| /---------------------- BOL-PanxαA
\----------------------+
\---------------------- Edu-PanxαA
Usage example 2
$: pb unrooted_panxA.nwk -rt Vpa-PanxαA
Output
[&R] ('Vpa-PanxαA':0.87256,('Lcr-PanxαA':0.77097,'Tin-PanxαA':0.81535)0.972:0.27115,(('Cfu-PanxαA':0.51865,'Lla-PanxαA':0.25913)0.994:0.2571,('BOL-PanxαA':0.23575,'Edu-PanxαA':0.38304):0.10821)0.190:0.14015)0.851;
Output tree
#### tree_1 ####
/-------------------------------------------------------------------- Vpa-PanxαA
|
| /---------------------- Lcr-PanxαA
|---------------------------------------------+
+ \---------------------- Tin-PanxαA
|
| /---------------------- Cfu-PanxαA
| /----------------------+
| | \---------------------- Lla-PanxαA
\----------------------+
| /---------------------- BOL-PanxαA
\----------------------+
\---------------------- Edu-PanxαA
Usage example 3
$: pb unrooted_panxA.nwk -rt Vpa-PanxαA Cfu-PanxαA
Output
[&R] (('Cfu-PanxαA':0.51865,'Lla-PanxαA':0.25913)0.994:0.2571,('Vpa-PanxαA':0.87256,('Lcr-PanxαA':0.77097,'Tin-PanxαA':0.81535)0.972:0.27115)0.851:0.14015,('BOL-PanxαA':0.23575,'Edu-PanxαA':0.38304):0.10821)0.190;
Output tree
#### tree_1 ####
/---------------------- Cfu-PanxαA
/---------------------------------------------+
| \---------------------- Lla-PanxαA
|
| /--------------------------------------------- Vpa-PanxαA
|----------------------+
+ | /---------------------- Lcr-PanxαA
| \----------------------+
| \---------------------- Tin-PanxαA
|
| /---------------------- BOL-PanxαA
\---------------------------------------------+
\---------------------- Edu-PanxαA