X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=a5e7a4ede8b0fbb77724bba444516251f353c12c;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=7b9ea960f3c6b979463cacc9e363ba5a6006ae44;hpb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;p=mothur.git

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 7b9ea96..a5e7a4e 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -125,8 +125,8 @@ int MatrixOutputCommand::execute(){
 								
 								data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 								//save values in similarity matrix
-								simMatrix[k][l] = data[0];
-								simMatrix[l][k] = data[0];
+								simMatrix[k][l] = 1.0 - data[0];  //convert similiarity to distance
+								simMatrix[l][k] = 1.0 - data[0];  //convert similiarity to distance
 							}
 						}
 					}