.fn.list and .an.list

Commands in mothur
1

Greeting,

I tried to learn how to make rarefaction curve by following two types of tutorial :

  1. Analysis sample : Agricultural soil community
  2. From this : ged.msu.edu/angus/files/lecture-metagenomics.pptx

I managed to follow the command until read.dist.

From those tutorial, it showed that I can get 3 types of file from command read.dist which are :

  1. Filename.fn.rabund
  2. Filename.fn.sabund
  3. Filename.fn.list

But, instead of this kind of file, I get :

  1. Filename.an.rabund
  2. Filename.an.sabund
  3. Filename.an.list

I tried to search the information in the website but I still don’t understand. Can anyone clear up this thing? How can I get .fn. file?

Thank you so much

2

fn indicates that the furthest neighbor clustering algorithm was used while an indicates that the average neighbor was used. Otherwise the file structures are the same. Based on our recent work, we no longer encourage people to use furthest neighbor since it inflates the number of OTUs.

3

I just read this information, so do you mean its better to use average neighbour for analysis rather than furthest analysis?

I see, because all of the tutorials that I browsed in the internet mostly used .fn. There is no one in my lab doing bacterial diversity, so all I can learn is via internet and your forum.

Thank you again.

4