Hi!
I have a protein alignement…and I would need to the OPU analysis… through " cluster" command …and I need to get the “. shared” file…for this I need a .names file…how could I build it without using the “unique” command?!
Thanks
at this point, mothur is ill suited for analyzing amino acid sequences. you’ll need to generate a distance matrix in protdist (from phylip) and then you can use that as a phylip-formatted matrix in cluster. you don’t need a names file to do this. you do need a group file, which you can make by hand or with a script.
Thanks Pat,
Now how do I know to which sequence the OTU refer too? This is what I have when I make a Shared file:
label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005
unique Cami_3_T1 1344 0 0 0 0 0
unique Cami_3_T2 1344 0 0 0 0 0
unique Cami_3_T3 1344 0 0 0 1 1
unique Cami_3_T4 1344 0 0 0 0 0
unique Tami_1_T2 1344 1 0 0 0 0
unique Tami_1_T3 1344 0 1 0 0 0
unique Tami_1_T4 1344 0 0 1 0 0
0.01 Cami_3_T1 1338 0 0 0 0 0
Who are the OTu001, Otu002 etc…?!
Thanks