#MSA via QUBO

These scripts convert a Fasta format input file representing sequences to align against each other. The qmsa.py script first calls msa2qubo.py which converts this input into a QUBO representation of a multiple sequence alignment algorithm. The QUBO file generated can then be run on a D-Wave simulator or on a D-Wave device itself. The results of the D-Wave (simulator) is a list of binary numbers, which are then interpreted using qubo2msa.py to show the results of the sequence alignment.

##Installation:

• Install python3 with numpy (python_anaconda is recommended)
• Add biopython to your python installation
• (Optional) Install qOp and add the bin directory to your PATH.
• (Optional) Install gurobi for integer quadratic programming option.

##Operating Instructions:

Type ./qmsa.py --help for instructions on how to run the script. The user is presented with options to specify lambda0, lamdba1 and lambda2.

##Licensing:

GNU GPL V3. See COPYING file for more details.

##Authors:

• Daniel Mapleson
• Luis Yanes
• Katie Barr
• Sophie Kirkwood
• Tim Stitt

##Acknowledgements:

D-Wave NASA