Scripts and data for "Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting"

Data folder

Each (sub)folder contains the following files:

• otu_table.txt: the OTU table (rarefied) file
• otu_table_taxonomy.txt: the OTU table (rarefied) file with taxonomic information. OTUs with the same taxa are collapsed toghether.
• sample_data.txt: the file containing the sample metadata
• taxonomy.txt: the file containing the taxonomy information for each OTU
• tree.tre: the phylogenetic tree in newick format

Script folder

The script folder contains the machine learning pipelines used in the paper. The scripts require Python >= 2.7, the NumPy, SciPy, Pandas, DendroPy, scikit-learn libraries and the PhyloRelief software. ml_lefse requires the LEfSe software (https://bitbucket.org/nsegata/lefse). Moreover, you neeed to set the variable lefse_path inside the script. ml_metaphyl requires the MetaPhyl software (http://www.cs.ucr.edu/~tanaseio/metaphyl.htm). Moreover, you neeed to set the variable metaphyl_path inside the script. Run script_name --help for additional information.