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  • Clustering a two-D matrix

    Hii All,

    I have generated a 2-D matrix based on NGS data which has cog scores in one axis (Y-axis) and sample no in other axis. Now i want to cluster this matrix based on the cog scores to find similarity between different sampling points and finally construct a UPGMA tree based on the output. Can any one suggest me a simple way to do this?? I don't have much knowledge about this...

    Thanks for any help in advance...

    Regards

    Chayan

  • #2
    Try MEGA: http://megasoftware.net/

    You should read the manual first to see if this would be appropriate to do with the dataset you have.

    Comment


    • #3
      You can use the Mclust package.

      (http://www.stat.washington.edu/mclust/)

      Change the parameter modelNames to obtain a suitable model (e.g., EII).

      Comment


      • #4
        thanks to both of you. As i am going through both the manuals, it will take some time as i am a hardcore biology guy, i want to clear one my query.. my matrix structure is like this
        A B C D E
        i 20 30 15 43 87
        ii 12 54 3 76 56
        iii 45 78 4 99 54

        now i want to cluster this based on the A, B, C, D, E based on the values of i, ii and iii...can i use "beta_diversity.py" from the qiime package..? then dont know basically how to generate to file format required for this as the prior steps are not same...


        thanks

        Comment


        • #5
          Originally posted by southan View Post
          You can use the Mclust package.

          (http://www.stat.washington.edu/mclust/)

          Change the parameter modelNames to obtain a suitable model (e.g., EII).
          thanks.. but i have never used R also... what i understand from the Mclust manual, if my matrix is like this

          A B C D E
          i 20 30 15 43 87
          ii 12 54 3 76 56
          iii 45 78 4 99 54

          i should use the modelName "VII"/"VVV" or other unequal volume or varying volume from the multivariate mixture??

          another thing, how to prepare the input file from the excel to feed into mclust??

          thanks a lot

          Comment

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