Monte Carlo Simulation

Program will call PHYLIP on the server to generate a neighbor-joining tree in Newick format and performs a bootstrap operation for a user-determined number of simulations, and report the confidence in each branch position.

Usage

Input

MSA file

Output

Confidence tree and consensus tree

Command to run this program

javac Phylip.java

java Phylip

Note

MSASequence.java and Confidence.java should be placed under the same directory where this program is being run.