Look at the tutorial, you can not directly import the list file using this command. You need to do a work around.

If I understand correctly this will import your list file

mothlist = system.file("extdata", "esophagus.fn.list.gz", package = "phyloseq")

This your group file

mothgroup = system.file("extdata", "esophagus.good.groups.gz", package = "phyloseq")

This your tree file (your NJ phylo tree from the clearcut command) 

mothtree = system.file("extdata", "esophagus.tree.gz", package = "phyloseq")

show_mothur_list_cutoffs(mothlist)

Than run the function is your question with the cutoff you want using the  list group and tree objects you generated. 

Personally I found it easier to just take the shared file and transform it to an OTU table and work my way from there. Where you basically have a tree file an OTU table and a metadata file.   

Hi Ido and thanks for your answer

Indeed, at the beginning, I was following the tutorial steps but they didn't work and failed just with the ".list" file. That's the reason I decided to try with the commands I wrote above and, actually they did work, except with that ".list" file.

When I "googled" about this issue I found there are more people with this problem but no answers.

I already have that OTU tables you mention, and I guess I will end up parsing and processing them by myself, but "phyloseq" looked promisingly easy and with awesome graphs!

Bests

BTW: I already checked my ".list" file and it is supposedly correct. It is as it comes out from mothur.

Hi Galo

Sorry I couldn't help more.

The graphs in phyloseq are great but they are mostly ggplot graphs so you can still work you way around good graphics. Phyloseq is somewhat underwhelming and restricting in my experience, don't think it brings much added value to the table compared to what's out there already. 

If you still wish to use phyloseq not all is lost, you can import the OTU table, taxonomy table and metadata table to phyloseq. Generate a phylogenetic tree of the representative sequences for each otu with clearcut or any other algorithm you want to use (you do that with the get.oturep command in mothur with fasta=true) and import that tree after that you can do everything with phyloseq. Just make sure to follow the tutorial and brake down the components so you could see the structure of the tables you need to generate. 

Ido

Thank you again Ido,

I think I will use my OTU-abundance tables to obtain the graphics and figures I want, (heatmaps, PCoA, barplots, etc).

I will look a little bit the web for packages capable to work from these tables and, if not, I think I will be able to do the work by myself.

Galo Adrián Goig : I hope you have solved the problem.

Mostly the problem could come from pre processing when the group/count file is not compatible with rest of the data.

mothur_ps