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A relabund file is similar to a shared file. The data in a relabund file represent relative abundance of an OTU over the samples. It is easiest to generate this file using the get.relabund command. The structure of a relabund file is analogous to an shared 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. final.an.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 relative abundance of each OTU from that group.
mothur > get.relabund(shared=final.an.shared)