RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2021 
FD November 01 
VO 31 
IS 11 
SP 2131 
OP 2137 
DO 10.1101/gr.275777.121 
UL http://genome.cshlp.org/content/31/11/2131.abstract 
AB 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.