The program included in this zip: 
1. WasThereHGT.py - This program receives 4 pairs of sequneces 2 pairs of of a witness gene and 2 pair of gene sequences of 
of suspected gene and based on Constant Relative Mutability detects whether the suspected gene undergone through HGT event.

To run the program with your own data you should assign gene sequences (with equal lengths for each pair) as follows:
the following variables should contain the following sequence data:
 
# r1r_gene r2r_gene - are 2 sequences of reference organisms' witness gene
# h1r_gene h2r_gene - are 2 sequences of a witness gene that belong to the organisms that carry the suspected HGT genes  
# r1h_gene r2h_gene - are 2 sequences of reference organisms' suspected gene
# h1r_gene h2r_gene - are 2 sequences of organisms with suspected HGT gene

All sequences should be with same length. 
sequence length should be indicated by assigning a value to the variable: n_of_nuc

A sample file - geneseq.txt is provided. This file contains with 8 sample sequences. The file should be located under \temp or
it location should be updated in the open command.

2. SampleSeq.py - This program generates 8 sample sequences of 70 nucleotides. By default the sequences are saved to a 
file geneseq.txt that is located under \temp directory.
If you wish to generate sequences with different length - please indicate in the variable n_of_nuc the requested length.

Note: SampleSeq.py  uses functions that are included in BuildGenF.py