bindiff | Compare two binary files

I computed the similarity between malware files using Bindiff, accordingly built a similarity matrix based on the pairwise similarity comparison. I want to cluster the results using scipy.cluster.hierarchy.linkage(y, method='single', metric='euclidean'), but the documentation says that y should be A condensed or redundant distance matrix. So, how can I convert the similarity matrix (NOT distance matrix) to the required format?

Where on this thread it's mention y can be he upper triangle of the distance matrix. But I want to point out that the order of comparison in Bindiff changes the result so similarity(file1,file2) != similarity(file2,file1)

so how can I overcome this issue?