Instructions for NewickTermBranch.pl

This program is designed to determine the external branch lengths of a Newick tree. Branch lengths are a measure of the amount of divergence between two nodes in the tree. The unit of the branch lengths is number of nucleotide (or amino acid) substitutions per site.

Input

  1. Newick tree file with branch lengths.

    Example:

    ((((((((((((a:0.00612000,b:0.00595500):0.01387200,c:0.01541200):0.01137700,((d:0.00893100,e:0.00854900):0.00682500,f:0.00684900):0.00199800):0.00000000,((g:0.02244900,((h:0.00345900,i:0.00515800):0.00706400,(j:0.00169600,k:0.00342400):0.00164900):0.00427000):0.00169100,l:0.01615600):0.00462800):0.00199400,(m:0.01245800,n:0.01418600):0.00353400):0.01074400,o:0.01140200):0.00864400,(p:0.00000000,q:0.00168400):0.01595200):0.01238600,(r:0.01226800,s:0.01613900):0.00124300):0.00201200,(t:0.05447700,u:0.01046900):0.00444700):0.05659400,OG1:0.12043000):0.04544800,og2:0.16630300):0.04016250,(og3:0.18159100,og4:0.11105600):0.02776250);

Output

  1. External branch lengths.

How to run

  1. Download NewickTermBranch.pl to your local computer, and set it to be executable by typing the following command in your working directory:

    chmod +x NewickTermBranch.pl

  2. Create a subdirectory in your working directory to hold input files. In the subdirectory, type following command:

    perl ../NewickTermBranch.pl NewickTreeFile