Description of Files for Sequence alignment:
Readme : The instructions for compiling and running a program

To generate your own data set:
1. Open sequence.h, set Gen to 1
2. make FGen
3.run FGen with the maximum length of the sequence desired and number of subsequences
4. Output files are set in assemble.cpp to change output files open and edit this file and repeat above steps.
5. There are 2 input files, sequence file and weight file (in this case these are output files).
6. There is one output file for contigs.
7. If you already have a sequence file, open sequence.cpp and edit the function createSeq to use the sequence file, NOTE: we will change this functionality later so that you don’t have to do these extra steps :)

To use a data set
1. Open sequence.h, set Gen to 0
2. make FGen 
3. There are 2 input files, sequence file and weight file. 
6. There is one output file for contigs.
4. run FGen with these 3 files, NOTE: We use fasta format, so please use the format so that the program can run correctly. Ex: ./FGen seq.dat weights.dat contigs.dat 
7. NOTE: we will change this functionality later so that you don’t have to do these extra steps :)
 

clus::  executable for clustering, takes two arguments size of original sequence, and no of subsequences    
Genome : executable for aligning, takes two arguments data file in fasta format and weight file in fasta format
FGen : Fuzzy Alignment
fastas_5  ,  fastasq_5   : data file in fasta format and weight file in fasta format
 RLE: executable for RLE
RLESeq.txt  : RLE output
sequencelcsvcluster2.cpp: main cpp file that calls all functions, you may need to edit this file to run the program with different options, please check the file for the options selected
 sequence.cpp    : sequence class file, functions implemented on sub sequences
  sequence.h        : header file
Display.cpp     : Display class, display has to be set to 1 in main cpp file, display is in html format in the file genome.html
Display.h : header file
lcs.cpp: File contains LCS functions and other string manipulation functions used in LCS                                                           
ReadMe : The instructions for compiling and running a program
Subseq.dat : Sample input file 
Weights.dat : Sample input file