We will be hosting mothur and R workshops throughout 2018. Learn more.

Phylotype

From mothur
Jump to: navigation, search

The phylotype command can be used to assign sequences to OTUs based on their taxonomy and outputs a .list, .rabund and .sabund files. To run through the example below, download Taxonomy Files.

Default settings

In order to run the phylotype() command, you need to generate a taxonomy file. You can do this using the classify.seqs command, enter the following command:

mothur > classify.seqs(fasta=abrecovery.fasta, template=silva.bacteria.fasta, taxonomy=silva.full.taxonomy)
mothur > phylotype(taxonomy=abrecovery.taxonomy)

This command will generate the following output:

mothur > phylotype(taxonomy=abrecovery.taxonomy)
1
2
3
4
5
6
7
8
9


Outputted to the screen is a level, 1 meaning the most specific taxonomy given.

Opening abrecovery.tx.list you would see the output as:

1	35      AY457915,AY457912,AY457898,AY457895,AY457894 ...			
2	35	AY457915,AY457912,AY457898,AY457895,AY457894,AY457891,AY457869 ... 
3	32	AY457915,AY457914,AY457912,AY457898,AY457895,AY457894,AY457891 ...		
4	25	AY457915,AY457914,AY457912,AY457898,AY457895,AY457894,AY457891,AY457888 ...
5	15	AY457915,AY457914,AY457913,AY457912,AY457908,AY457901,AY457898,AY457895 ...
6	11	AY457915,AY457914,AY457913,AY457912,AY457908,AY457901,AY457898,AY457895 ...
7	8	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457908,AY457901,AY457898 ...
8	5	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457908,AY457901,AY457898 ...
9	1	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457909,AY457908,AY457907 ...

Options

label

The labels count up from the leaves to the root of the phylotree. There may only be a couple of level in your phylotree that you are interested in seeing. You can use the label option to specific the levels you would like. If you want the data for the lines labeled unique, 1, 3 and 5 you would enter:

mothur > phylotype(taxonomy=abrecovery.taxonomy, label=1-3-5)
1
3
5

Opening abrecovery.tx.list you would see the output as:

1	35      AY457915,AY457912,AY457898,AY457895,AY457894 ...			
3	32	AY457915,AY457914,AY457912,AY457898,AY457895,AY457894,AY457891 ...		
5	15	AY457915,AY457914,AY457913,AY457912,AY457908,AY457901,AY457898,AY457895 ...

cutoff

The cutoff parameter counts up from the root to the leaves of the phylotree. The cutoff parameter can be used to truncate the depth of the taxonomy you are interested in.

mothur > phylotype(taxonomy=abrecovery.taxonomy, cutoff=6)
1
2
3
4
5
6

Opening abrecovery.tx.list you would see the output as:

1	25	AY457915,AY457914,AY457912,AY457898,AY457895,AY457894,AY457891,AY457888 ...
2	15	AY457915,AY457914,AY457913,AY457912,AY457908,AY457901,AY457898,AY457895 ...
3	11	AY457915,AY457914,AY457913,AY457912,AY457908,AY457901,AY457898,AY457895 ...
4	8	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457908,AY457901,AY457898 ...
5	5	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457908,AY457901,AY457898 ...
6	1	AY457915,AY457914,AY457913,AY457912,AY457911,AY457910,AY457909,AY457908,AY457907 ...

Level 1 was level 4 without the cutoff, but now the most specific taxonomy given has changed since we truncated the tree.


name

The name option allows you to add a names file so your list file will contain all your sequences, not just the unique ones.

mothur > phylotype(taxonomy=abrecovery.taxonomy, name=abrecovery.names)

Revisions

  • 1.25.0 - the numOtus in the list file is one to high. Otus are clustered correctly, the count is just off.
  • 1.25.0 - only clustering at leaf nodes, level 1.
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350