Re ANOSIM and AMOVA input files

Hi Guys

Can anyone point me to how to get/make the correct dist and design files for ANOSIM and AMOVA - the wiki page has no info



You can calculate OTU-distance matrices using the dist.shared command with your shared file. IF you want phylogenetic distances you can use either of the unifrac commands with the ‘distance=lt’ parameter set.

Design files are just a simple tab delimited file with lines of “Sample->Grouping”.

HI dwaite - Thanks for getting back to me.

In the amazon tutorial data file for AMOVA, the design file looks like it links all the sequences to a sample e.g.
U68589 A
U68590 A
U68591 A
U68592 A
U68593 A
U68639 B
U68640 B
U68641 B
U68642 B
U68643 B
U68644 B
U68645 B

while in the dune files, provided for the ANOSIM tutorial, it looks like samples are linked to a group in the design file.
2 BF
13 SF
4 SF
16 SF
6 HF
1 SF
8 HF

so the design files, even though they are called the same thing are in fact slightly different and are used to test different aspects.

So my question is this - does AMOVA really look at one sample’s molecular diversity compared to another - so uses alpha diversity, while ANOSIM compares samples from a group to samples from another group and uses the beta/phylogenetic diversity to see if they are the same?

If this is correct then I can use the group file as the design file for AMOVA and just make a simple samples linked to groups that I wish to test for ANOSIM?



You can do them either way - using sequences to see if there’s a difference between two samples, or using samples to see if there’s differences between groups of samples.