Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.

"data availability all data used in this work are available at https://github com/bin-ma/bd-rpc/tree/master/example collected from ncbi ( http://ncbi nlm nih gov ) and gisaid ( https://www gisaid org/ )."

"finally a user-friendly website ( http://www bd-rpc xyz ) is available for users to classify new samples instantly and facilitate exploration of the phylogenetic research in viruses and the bd-rpc is available on github ( http://github com/bin-ma/bd-rpc ) phylogenetic tree recoding insertion/deletion new sample placement simulated annealing phylogenetic relationships among species have a pivotal role in almost every branch of biology ( ; ).; in this study all analyses were run on a 40-core ubuntu 18 04 5 system with 187 gb of ram and the code is available on github ( http://github com/bin-ma/bd-rpc ).; data availability all data used in this work are available at https://github com/bin-ma/bd-rpc/tree/master/example collected from ncbi ( http://ncbi nlm nih gov ) and gisaid ( https://www gisaid org/ ).; the source code and user manual are available at https://github com/bin-ma/bd-rpc . the clinical data and taxonomy information were collected by python scripts and manual adjustments were made afterward ( supplementary table s1 and supplementary table s2 )."

"Conflict of interest: The authors declare no competing interests."

"This work was supported by grants from the National Key Research and Development Program of China (2022YFD1801005), the National Natural Science Foundation of China (32272989), Natural Science Foundation of Hubei Province (2021CFA016), the earmarked fund for CARS-41, Hubei Province Natural Science Foundation for Distinguished Young Scholars (2020CFA060), and Applied Basic Research Project of Wuhan (Grant No. 2020020601012254)."