iTol.py

Create files appropriate for use in the iTOL visualization program by using the abundance data from a biom-format file and groups specified in a QIIME mapping file. The program also modifies a Newick-format phylogenetic tree file to use proper taxonomic names instead of OTU IDs for useful display in iTOL.

usage: iTol.py [-h] -i OTU_TABLE -m MAPPING [-t INPUT_TREE] [-e OUTPUT_TRE] [-o OUTPUT_ITOL_TABLE] [-c MAP_CATEGORIES] [-a {MRA,NMRA,raw}]

Required arguments

-i OTU_TABLE, --otu_table OTU_TABLE

The biom-format file with OTU-Sample abundance data.

-m MAPPING, --mapping MAPPING

The mapping file specifying group information for each sample.

Optional arguments

-t INPUT_TREE, --input_tree INPUT_TREE

A phylogenetic tree in Newick format to be modified by exchanging the OTU ID node names for taxonomic names.

-e OUTPUT_TRE, --output_tre OUTPUT_TRE

The output Newick-format tree (.tre) file

-o OUTPUT_ITOL_TABLE, --output_itol_table OUTPUT_ITOL_TABLE

Other than a phylogenetic tree, the main input to iTOL is a dataset file containing some representation of the abundance of every OTU across the specified data groups. This program provides multiple calculation methods. See the –analysis_metric option for details.

-c MAP_CATEGORIES, --map_categories MAP_CATEGORIES

Any mapping categories, such as treatment type, that will be used to group the data in the output iTOL table. For example, one category with three types will result in three data columns in the final output. Two categories with three types each will result in six data columns. Default is no categories and all the data will be treated as a single group.

-a {MRA,NMRA,raw}, --analysis_metric {MRA,NMRA,raw}

Specifies which metric is calculated on the abundance data in the OTU table. Available options: MRE - mean relative abundance (Abundance data is normalized by total sample abundance, then averaged across OTU), NMRE - normalized mean relative abundance (MRE normalized by the total MRE across the groups as specified in –map_categories), raw (outputs the actual sequence abundance data for each OTU).

--stabilize_variance

Apply the variance-stabilizing arcsine square root transformation to the OTU proportion data. Recommended for usage with -a NMRA or -a MRA.

-h, --help

Show the help message and exit.

Workflow for generating useful phylogenetic trees using PhyloToAST

Step 1 : Obtain .tre file from QIIME’s make_phylogeny.py script.

Step 2 : Run iTol.py script with -a NMRA analysis metric. This file will denote the multibar graph around the circular phylogenetic tree.

Step 3 : Run iTol.py script with -a raw analysis metric. This file will denote the gradient graph around the circular phylogenetic tree.

Step 4 : Upload modified .tre file from iTol.py script to iTOL website. Add your dataset files and obtain the final phylogenetic tree figure.

Example output image

NOTE : Please refer to iTOL help page for changing dataset parameters.