I have been using megan for metagenomic analysis for quite a while now. I wanted to calculate the alpha diversity indices (shannon, chao1 and simpson) for my data but cannot find such option in megan. I want to get the values of alpha diversity indices.
Kindly guide me through this problem. I will be very much thankful to you.
Select the nodes on which you want to base the calculation and then use one of the two following menu items in the Options menu:
Shannon-Weaver Index
Simpson-Reciprocal index
So, two out of the three that you named.
I took a quick look at the Chao1 index. I am not sure that it is appropriate for MEGAN in general. It uses the number of species to which 1 or 2 reads have been assigned to estimate now many further species might be in the sample, just below the level of detection. While that makes sense for moderate numbers of full length 16S sequences, I don’t think that this makes sense for metagenomic data, which is the main focus of MEGAN.