Refereed journal article or data article (A1)

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

List of Authors: Armstrong George, Cantrell Kalen, Huang Shi, McDonald Daniel, Haiminen Niina, Carrieri Anna Paola, Zhu Qiyun, Gonzalez Antonio, McGrath Imran, Beck Kristen L, Hakim Daniel, Havulinna Aki S, Meric Guillaume, Niiranen Teemu, Lahti Leo, Salomaa Veikko, Jain Mohit, Inouye Michael, Swafford Austin D, Kim Ho-Cheol, Parida Laxmi, Vázquez-Baeza Yoshiki, Knight Rob

Publisher: Cold Spring Harbor Lab Press, Publications Dept

Publication year: 2021

Journal: Genome Research

Journal name in source: GENOME RESEARCH

Journal acronym: GENOME RES

Volume number: 31

Issue number: 11

Number of pages: 7

ISSN: 1088-9051

eISSN: 1549-5469


The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.

Last updated on 2021-10-12 at 09:31