Sparse unifrac algorithm for the study of microbial beta diversity
Year: 2012
Type: dissertation
Abstract: This document de nes an algorithm that allows beta diversity calculations
on sparse data and presents the results obtained.
Sparse UniFrac algorithm reads a phylogenetic tree and calculates a distance
vector only for the nodes that are relevant on the UniFrac distance calculation.
Then makes dense column slices of the sparse data matrix to calculate the
UniFrac distance between them.
Data with variable observations, samples and density con guration is pro-
cessed using sparse UniFrac and the results show a diminution of memory usage
compared with the current UniFrac code. This decrease in memory usage solves
some of the current problems which are present trying to calculate UniFrac dis-
tance with a large amount of data.
Author: Juan Ansuategui Vicente
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W223708252