GAUGE
 Performs Gene coupling analysis, calculates slightely correlated and highly correlated reaction pairs, finds maximum number of 
inconsistent reaction pairs which can be resolved, finds minimum number of reactions for addition to the model and finds alternative optimal solutions.

GAUGE requires COBRA toolbox, F2C2 package and Tomlab_cplex solver.

Usage:

[alternatives,f_max,f_min]=GAUGE(model,PCC,F2C2_Solver,SC_PCC,HC_PCC,U)
 INPUTS:
   model: metabolic model in COBRA format with known gene_reaction
       associations in model.rules and model.rxnGeneMat field
   PCC: a matrix containing pearson correlation coefficients of gene pairs
       number of columns=number of rows=number of genes in the model
       PCC(i,j)=pearson correlation coefficient of gene pair (i,j)
   F2C2_solver: the solver which is used in F2C2 function, (glpk,Lindo,clp,SoPlex,linprog)
   SC_PCC: cutoff for choosing slightly correlated reaction pairs
   HC_PCC: cutoff for choosing highly correlated reaction pairs
   U: structure representing universal dataset of reactions with 3 fields
       U.S: stoichiometric matrix of the reactions in the database
       U.lb: lower bounds of reactions
       U.ub: upper bounds of reactions
 OUTPUTS:
   alternatives: all of the alternative solutions. each column shows a
       possible solution
   f_min: minimum number of reactions which should be added to the model
   f_max: maximum number of inconsistancies which can be resolved