TY  - JOUR
A1  - Armstrong, George
A1  - Cantrell, Kalen
A1  - Huang, Shi
A1  - McDonald, Daniel
A1  - Haiminen, Niina
A1  - Carrieri, Anna Paola
A1  - Zhu, Qiyun
A1  - Gonzalez, Antonio
A1  - McGrath, Imran
A1  - Beck, Kristen L.
A1  - Hakim, Daniel
A1  - Havulinna, Aki S.
A1  - Méric, Guillaume
A1  - Niiranen, Teemu
A1  - Lahti, Leo
A1  - Salomaa, Veikko
A1  - Jain, Mohit
A1  - Inouye, Michael
A1  - Swafford, Austin D.
A1  - Kim, Ho-Cheol
A1  - Parida, Laxmi
A1  - Vázquez-Baeza, Yoshiki
A1  - Knight, Rob
T1  - Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
Y1  - 2021/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2131 
EP  - 2137 
DO  - 10.1101/gr.275777.121 
VL  - 31 
IS  - 11 
UR  - http://genome.cshlp.org/content/31/11/2131.abstract 
N2  - 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. 
ER  -