Software for Small Phylogeny Construction using Pathgroups

Introduction

• Input:

  As in the sample test data here, the format for the input file:

  1. Each line represents a chromosome, and there is at least one space between two successive genes.

  2. A gene name can be any string without spaces. A default + understood for all the genes on one of the strands, but an explicit - sign must be added to all genes located on the other strand.

• Output:

   

  1. Gene orders for reconstructed ancestors.

  2. Branch lengths in terms of rearrangement distance.

• To run the program:

  1. Download and unzip the zipped file here

  2. Direct the terminal to folder smallPhylogeny, which contains the java scripts

  3. Compile and run the program:

      

     • javac *.java

     • java TestSmallPhylogeny > result.txt

  4. Check the output in the result.txt file

• To test other sets of genomes

  1. Change the "Section 1: read in input genomes" in TestSmallPhylogeny.java file to read in your data properly.

  2. Change the "Section 2: set the tree structure" in TestSmallPhylogeny.java file according to your specific tree.

  3. Compile and run the program again.