# make.shared

The make.shared command reads a list and group file or biom file and creates a .shared file as well as a rabund file for each group.

## Inputting list data for multiple samples

The Amazonian data set actually represents sequences from two samples - one from soil collected at a pasture site and a rainforest site. Looking at the file amazon.groups you can see which sequences belong to the pasture and rainforest sites. There is no limit to the number of groups you can have.

mothur > make.shared(list=98_sq_phylip_amazon.an.list, group=amazon.groups)


or if you used a count file instead of a name file and group file:

mothur > make.table(name=amazon.names, group=amazon.groups)
mothur > cluster(phylip=98_sq_phylip_amazon.dist, count=amazon.count_table)
mothur > make.shared(list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)


or you can convert a count file to a shared file and list file where each representative sequence is placed in it’s own OTU. This is the same thing as generating a shared file of ASVs

mothur > make.shared(count=amazon.count_table, label=asv)


This command will generate a shared file.

## Creating a shared file from a biom file

You can also convert a biom file to a shared file to import your data into mothur.

mothur > make.shared(biom=example.biom)


## Options

### label

There may only be a couple of lines in your OTU data that you are interested in summarizing. There are two options. You could: (i) manually delete the lines you aren’t interested in from you rabund, sabund, list, or shared file; (ii) or use the label option. If you only want to read in the data for the lines labeled unique, 0.03, 0.05 and

0.10 you would enter:

mothur > make.shared(list=98_sq_phylip_amazon.fn.list, group=amazon.groups, label=unique-0.03-0.05-0.10)


### groups

You can use the groups parameter to specify which groups you want included in your analysis:

mothur > make.shared(list=98_sq_phylip_amazon.fn.list, group=amazon.groups, groups=forest-pasture)


## Revisions

• 1.22.0 Removed ordergroup parameter.