huda Posted August 18, 2012 Share Posted August 18, 2012 hi, If I have similarity matrix that I got it from sequence alignment, where each element of this matrix repersent the rate of similarity .i.e the max score represent mas similarity. say n*n symmetric that show the rate of similarity among n objects . ex. x=[10 3 2 3 6 4 2 4 5]; here obj. 1 is most similar to obj. 2 because the max score except diagonal(10) is 3 and so on. the diagonal here is represent the comparison the object with itsel so has the max value if I used distance metric such euclidean distance to cluster these objects, is it best to set the diagonal to zero, or leave it ? by the way , which the best way to cluster the similarity matrix that result from sequence alignment? Link to comment Share on other sites More sharing options...
Phi for All Posted August 18, 2012 Share Posted August 18, 2012 ! Moderator Note Please, just post your thread once in a single section. Multiple instances makes it very difficult to follow the discussion. Link to comment Share on other sites More sharing options...
huda Posted August 18, 2012 Author Share Posted August 18, 2012 ! Moderator Note Please, just post your thread once in a single section. Multiple instances makes it very difficult to follow the discussion. what I have to do now? Link to comment Share on other sites More sharing options...
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