A shared file is analogous to an rabund file. The data in a shared file represent the number of times that an OTU is observed in multiple samples. It is easiest to generate this file using the make.shared command. The structure of a shared file is analogous to an rabund file. The first column contains the label for the comparison - this will be the value for the first column of each line from the original list file (e.g. patient70.fn.list). The second column contains the group name that designates where the data is coming from for that row. Next is the number of OTUs that were found between each of the groups and is the number of columns that follow. Finally, the remaining columns indicate the number of sequences that belonged to each OTU from that group. The list files that are generated from this command contain the sequence names in each OTU for each group and can be processed using commands such as collect.single() like any other list files.
Sample output of 98_sq_phylip_amazon.fn.shared, which can be downloaded in the amazondata.zip file:
label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 ... 0.10 forest 55 0 5 2 3 1 1 3 3 1 0 ... 0.10 pasture 55 7 2 5 1 3 2 0 0 1 2 ...