phylotype
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 Example Data and mothur-formatted version of the RDP training set (v.9).
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=final.fasta, count=final.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax)
mothur > phylotype(taxonomy=final.taxonomy)
This command will generate the following output:
mothur > phylotype(taxonomy=final.taxonomy)
1
2
3
4
5
6
Outputted to the screen is a level, 1 meaning the most specific taxonomy given.
Opening final.tx.list you would see the output as:
label numPhylos Phylo01 Phylo02 Phylo03 Phylo04 Phylo05 Phylo06 Phylo07 Phylo08 ...
1 63 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
2 39 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
3 24 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
4 15 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
5 9 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
6 1 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
Options
count
The count option allows you to provide a count file associated with your taxonomy file.
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=final.taxonomy, label=1-3-5)
1
3
5
Opening final.tx.list you would see the output as:
label numPhylos Phylo01 Phylo02 Phylo03 Phylo04 Phylo05 Phylo06 Phylo07 Phylo08 ...
1 63 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
3 24 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
5 9 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
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=final.taxonomy, cutoff=4)
1
2
3
4
Opening final.tx.list you would see the output as:
label numPhylos Phylo01 Phylo02 Phylo03 Phylo04 Phylo05 Phylo06 Phylo07 Phylo08 ...
1 63 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
2 39 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
3 24 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
4 15 M00967_43_000000000-A3JHG_1_1101_10331_23332,M00967_43_000000000-A3JHG_1_1101_10367_17664,...
Level 1 was level 4 without the cutoff, but now the most specific taxonomy given has changed since we truncated the tree.
name - not recommended
The name option allows you to provide a name file associated with your taxonomy file.
We DO NOT recommend using the name file. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.
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