get.otulist

The get.otulist command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU. For this tutorial you should download and decompress amazondata.zip.

Default settings

mothur > get.otulist(list=98_lt_phylip_amazon.fn.list)

This will result in output to the screen looking like:

unique
0.00
0.01
0.02
0.03
0.04
0.05
0.06
...

Options

label

There may only be a couple of lines in your OTU data that you are interested in. You can either manually delete the lines you aren’t interested in from your list file or use the label option. If you want the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:

mothur > get.otulist(list=98_lt_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10)
unique
0.03
0.05
0.10

Opening 98_lt_phylip_amazon.fn.0.03.otulist you would see the output as:

1  U68589
2  U68590
3  U68591
4  U68592
5  U68593
6  U68594
7  U68595
8  U68596
9  U68597
10 U68598
11 U68599
12 U68600
13 U68601
14 U68637,U68602
15 U68603
16 U68605
...

sort

The sort parameter allows you to select how you want the output displayed. Options are otu and name, otu is the default. If otu is selected the output will be otu number followed by the list of names in that otu. If name is selected the output will be a sequence name followed by its otu number.

mothur > get.otulist(list=98_lt_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10, sort=name)

Opening 98_lt_phylip_amazon.fn.0.03.otulist you would see the output as:

U68589 1
U68590 2
U68591 3
U68592 4
U68593 5
U68594 6
U68595 7
U68596 8
U68597 9
U68598 10
U68599 11
U68600 12
U68601 13
U68637 14
U68602 14
U68603 15
...