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Various problems with your implementation of UPGMA

Dear Huy,

I tried to run both your GPU and CPU implementations of UPGMA, but, I experienced various problems:

  • GPU compiles but it produces a segmentation fault (probably, at line 299)
  • CPU compiles and runs accurately. Nevertheless, there are two issues:
  1. You have not included a Phylip file parser. Instead, you use a preset 2D array a (line 75) which is of no use, as users have their own distance files (in Phylip format).
  2. You do not input the names of the leaves, so the Newick output lacks their names:
    ((((: 4, : 4): 4.25, ((: 0.5, : 0.5): 5.75, : 6.25): 2): 6.25, : 14.5): 2.5, : 17)
    instead of:
    ((((Turtle:4,Chicken:4):4.25,((Man:0.5,Monkey:0.5):5.75,Dog:6.25):2):6.25,Tuna:14.5):2.5,Moth:17);

I would be indebted, if you could fix the bug and add the functionalities that would make your tool a great addition in bioinformatics algorithms. In that case, please, let me know how I can cite your implementations.

Best Regards,
Dr Ioannis Michalopoulos

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