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.