TY - GEN
T1 - Scalable and Accurate Phylogenetic Placement Using pplacer-XR
AU - Wedell, Eleanor
AU - Cai, Yirong
AU - Warnow, Tandy
N1 - Publisher Copyright:
© 2021, Springer Nature Switzerland AG.
PY - 2021
Y1 - 2021
N2 - Phylogenetic placement, the problem of placing a sequence into a precomputed phylogenetic “backbone” tree, is useful for constructing large trees, performing taxon identification of newly obtained sequences, and other applications. The most accurate current method, pplacer, performs the placement using maximum likelihood but fails frequently on backbone trees with 5000 sequences. We show a simple technique, pplacer-XR (pplacer-eXtra Range), that extends pplacer to large datasets. We show, using challenging large datasets, that pplacer-XR provides the accuracy of pplacer and the scalability to ultra-large datasets of a leading fast phylogenetic placmement method, APPLES. pplacer-XR is available in open source form on github.
AB - Phylogenetic placement, the problem of placing a sequence into a precomputed phylogenetic “backbone” tree, is useful for constructing large trees, performing taxon identification of newly obtained sequences, and other applications. The most accurate current method, pplacer, performs the placement using maximum likelihood but fails frequently on backbone trees with 5000 sequences. We show a simple technique, pplacer-XR (pplacer-eXtra Range), that extends pplacer to large datasets. We show, using challenging large datasets, that pplacer-XR provides the accuracy of pplacer and the scalability to ultra-large datasets of a leading fast phylogenetic placmement method, APPLES. pplacer-XR is available in open source form on github.
KW - Likelihood-based methods
KW - Phylogenetic placement
KW - Phylogenetics
UR - http://www.scopus.com/inward/record.url?scp=85111087512&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85111087512&partnerID=8YFLogxK
U2 - 10.1007/978-3-030-74432-8_7
DO - 10.1007/978-3-030-74432-8_7
M3 - Conference contribution
AN - SCOPUS:85111087512
SN - 9783030744311
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 94
EP - 105
BT - Algorithms for Computational Biology - 8th International Conference, AlCoB 2021, Proceedings
A2 - Martín-Vide, Carlos
A2 - Vega-Rodríguez, Miguel A.
A2 - Wheeler, Travis
PB - Springer
T2 - 8th International Conference on Algorithms for Computational Biology, AlCoB 2021
Y2 - 7 June 2021 through 11 June 2021
ER -