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@amynang I declined the pull request as I think the while(TRUE) within the function can lead to unexpected behavior. The original problem was probably an isolated component in the input. I added this check to before assembly:::.move() is called for the first time to make sure this does not happen. I added your suggestions, but without the while loop; this is because, if the move is not valid because of an isolated species or component, the move is discarded: return(sp.names). If you try to force the move to have a solution and it doesn't, you get stick into move() indefinitely.

The new commit should fix the issue you were having.

Hey,
similarity filtering behaves strangely, selecting groups of species that are really similar but dissimilar from other groups. I suspect the reason is that the algorithm is trying to minimize the sum of similarity not the average?

example