classify.tree
The classify.tree command is used to get a consensus taxonomy for each node on a tree.
Default Setting
The classify.tree command parameters are tree, taxonomy, name, group and cutoff. The taxonomy and tree parameters are required.
First you must classify your sequences, you can do so by running the following command:
mothur > classify.seqs(fasta=abrecovery.fasta, template=trainset6_032010.rdp.fasta, taxonomy=trainset6_032010.rdp.tax)
Then create a tree:
mothur > dist.seqs(fasta=abrecovery.align, output=lt)
mothur > clearcut(phylip=abrecovery.phylip.dist)
Then you can use your taxonomy file to find the consensus taxonomy for your tree nodes.
mothur > classify.tree(taxonomy=abrecovery.rdp.taxonomy, tree=abrecovery.phylip.tre)
When you open abrecovery.phylip.taxonomy.summary you will see:
TreeNode NumRep Taxonomy
243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
...
The first column is the tree node label, the second column is the number of descendants of the node and the third column is the consensus taxonomy.
name
The name parameter allows you add a name file with your taxonomy file.
mothur > classify.tree(taxonomy=abrecovery.rdp.taxonomy, tree=abrecovery.phylip.tre, names=abrecovery.names)
group
The group parameter allows you to provide a group file. If a group file is given, a consensus for each group will be given at each node.
mothur > classify.tree(taxonomy=abrecovery.rdp.taxonomy, tree=abrecovery.phylip.tre, group=abrecovery.groups)
cutoff
The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.
mothur > classify.tree(taxonomy=abrecovery.rdp.taxonomy, tree=abrecovery.phylip.tre, cutoff=80)
Revisions
- 1.24.0 - First introduced.
- 1.31.0 - Bug Fix: when name file is given everything is unclassified - https://forum.mothur.org/viewtopic.php?f=3&t=2161&p=6116#p6116
- 1.40.0 Allow for () characters in taxonomy definitions. #350