rarefaction curve

Commands in mothur
1

Good afternon,
I need a help to build a rarefaction curve.
As I understood an input file should be a distance matrix (Phylip).
but I do not understand how should the command looks like to
open my matrix.

Thank you

2

Did you get a chance to look at the examples on the wiki? http://www.mothur.org/wiki/Rarefaction.single and http://www.mothur.org/wiki/Rarefaction.shared should be helpful, but to get you started…

The command to read in your distance file is read.dist and should look like:

read.dist(phylip=yourFileName)

Then you need to generate a .list file by clustering the distance matrix with the cluster command:

cluster()

Then you can read the list file:

read.otu(list=theListFileGenerateByCluster)

Then the to generate the rarefaction curve:

rarefaction.single()

Hope this helps!