rootstrap.py: A script to calculate the rootstrap support values for all the branches

Dependencies:

       ete3

       Biopython

       dendropy

Syntax:

rootstrap.py <tree file> <bootstrap trees file> <is rooted> <outgroup file>

<treefile>                     The tree file where you want to calculate the rootstrap support values in Newick format (e.g. tree.treefile).
                                       The tree can be rooted or unrooted.

<bootstrap trees file> All the bootstrap trees in Newick format.
                                      For example: .ufboot file from IQ-TREE (tree.ufboot)

<is rooted>                  Are the ML tree and the boostrap trees rooted or not.
                                      True - The trees assumed to be rooted and no outgroup taxa infromation is required
                                      False - The trees assumed to be unrooted and outgroup taxa infromation is required
                                      (default: True)

<outgroup file> ;              outgroup taxa in Nexus format.
                                      The outgroup block can be part of the alignment (e.g. OG_File1.nex) file or in a separate file (e.g. OG_File2.nex)

---

rBED_rSED.py: A script to calculate the root Branchlength Error Distance (rBED) and the root Split Error Distance (rSED)

Syntax:

rBED_rSED.py <tree file>

<treefile>                     The tree file (rooted tree only in Newick format) where you want to calculate rBED and rSED values.

Note: In order to calculate rBED and rSED values, the true root should be known (or assumed to be known) in advance.