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Other Scripts
Geut Galai edited this page Jan 25, 2023
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Here are described scripts that are not part of the pipeline. For example They are run only once, to produce data to be used.
This script analyses the DNA sequances of all the ASVs in the data to create a phylogenetic tree. It saves it to a file as an r object (.rds) to be used in the future.
output/ASV_full_taxa.csv: The phylogenetic classification of each microbial element sampled - contains the DNA sequance.
output/njs_distances_for_all_asvs_phylo.rds: An R object containing a naive tree produced using neighbor-joining from a distance matrix.
output/fitted_asvs_phylo_tree.rds: An R object containing an optimized phylogenetic tree. It is an object of class 'pml'.