TY - JOUR
T1 - DecentTree
T2 - scalable Neighbour-Joining for the genomic era
AU - Wang, Weiwen
AU - Barbetti, James
AU - Wong, Thomas
AU - Thornlow, Bryan
AU - Corbett-Detig, Russ
AU - Turakhia, Yatish
AU - Lanfear, Robert
AU - Minh, Bui Quang
N1 - Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press.
PY - 2023/9/1
Y1 - 2023/9/1
N2 - Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which Neighbour-Joining is a useful approach, new implementations of existing methods are warranted. Results: Here, we present DecentTree, which provides highly optimized and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g. it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g. RapidNJ) when generating a tree of 64 000 SARS-CoV-2 genomes.
AB - Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which Neighbour-Joining is a useful approach, new implementations of existing methods are warranted. Results: Here, we present DecentTree, which provides highly optimized and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g. it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g. RapidNJ) when generating a tree of 64 000 SARS-CoV-2 genomes.
UR - http://www.scopus.com/inward/record.url?scp=85170438733&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btad536
DO - 10.1093/bioinformatics/btad536
M3 - Article
SN - 1367-4803
VL - 39
JO - Bioinformatics
JF - Bioinformatics
IS - 9
M1 - btad536
ER -