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The input to this step is a distance matrix (i.e. resulting file from beta_diversity.py).
Usage: neighbor_joining.py [options]
The output is a newick formatted tree compatible with most standard tree viewing programs. Batch processing is also available, allowing the analysis of an entire directory of distance matrices.
neighbor joining (nj) cluster (Single File):
To perform nj clustering on a single distance matrix (e.g.: beta_div.txt, a result file from beta_diversity.py) use the following idiom:
neighbor_joining.py -i beta_div.txt -o beta_div_cluster.tre
neighbor joining (Multiple Files):
The script also functions in batch mode if a folder is supplied as input. This script operates on every file in the input directory and creates a corresponding neighbor joining tree file in the output directory, e.g.:
neighbor_joining.py -i beta_div_weighted_unifrac/ -o beta_div_weighted_clusters/