bayestraitswrap Files

Citation: 
Sklenarova K, Chesters D, Bocak L (2013) 
Phylogeography of Poorly Dispersing Net-Winged Beetles: A Role of Drifting India in the Origin of Afrotropical and Oriental Fauna. 
PLoS ONE 8(6): e67957. doi:10.1371/journal.pone.0067957


if you use BayesTraits and you get tired of the effort required in defining each node, this is the script for you.

input is a fully bifurcating, rooted tree, in newick format. 
branchlengths and node support values are ignored, if present.
do not use only numbers for terminals id's,
should contain other characters.

to run:
perl bayestraitswrap.pl [input_tree]

e.g.
perl bayestraitswrap.pl my_tree.nwk

output is a table of BayesTraits format node definitions 
for each node found in your input tree.
the output file is called scriptOUT, and each row has a single node, e.g
AddNode NODE_3	348PLATYCIS 578LOPHEROS
'AddNode' is the appropriate command for BayesTraits to analyse a 
node only where it is present, this is followed by the name 
of the node (which is arbitrary), 
and then the terminals that belong to that node.
also printed is newick_nodekey.nwk, you can read this with
any tree viewing software and observe the node labels.
the node labels (numbers) correspond to the node definitions in scriptOUT.
so the user can find the nodes of interest by viewing the tree 
in newick_nodekey.nwk, the get the corresponding command to analyse 
that node, from within the scriptOUT file. 
this is illustrated in example.pdf, which shows the newick tree
as viewed in a tree viewer, and the scriptOUT file.