Figures
Inserting genetic sequences into a phylogenetic tree.
The rate of genome sequencing and availability has rapidly increased. It is anticipated that conventional de novo phylogenetic inference may no longer be efficient for such an increasing number of sequences. By integrating parsimony analysis with pre-computed ancestral sequences, we developed TIPars, which allows rapid and memory-efficient insertion of sequences into a reference phylogeny at high accuracy. This enables real-time monitoring of pathogen transmission during a pandemic using large-scale global phylogenetic analysis such as those demonstrated in COVID-19 pandemic. Ye et al 2024
Image Credit: Ningqi Zhao (jeaning7@d24h.hk), Yongtao Ye (yytao@connect.hku.hk), Marcus H. Shum (hohin2@d24h.hk) and Tommy Tsan-Yuk Lam (ttylam@hku.hk) should be credited with the creation of the image.
Citation: (2024) PLoS Computational Biology Issue Image | Vol. 20(2) March 2024. PLoS Comput Biol 20(2): ev20.i02. https://doi.org/10.1371/image.pcbi.v20.i02
Published: March 1, 2024
Copyright: © 2024 . This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The rate of genome sequencing and availability has rapidly increased. It is anticipated that conventional de novo phylogenetic inference may no longer be efficient for such an increasing number of sequences. By integrating parsimony analysis with pre-computed ancestral sequences, we developed TIPars, which allows rapid and memory-efficient insertion of sequences into a reference phylogeny at high accuracy. This enables real-time monitoring of pathogen transmission during a pandemic using large-scale global phylogenetic analysis such as those demonstrated in COVID-19 pandemic. Ye et al 2024
Image Credit: Ningqi Zhao (jeaning7@d24h.hk), Yongtao Ye (yytao@connect.hku.hk), Marcus H. Shum (hohin2@d24h.hk) and Tommy Tsan-Yuk Lam (ttylam@hku.hk) should be credited with the creation of the image.