Evidence map›Paper›PMID 38361823›Full record

ArticleVirus evolution2024

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

Bin Ma, Huimin Gong, Qianshuai Xu, Yuan Gao, Aohan Guan, Haoyu Wang, Kexin Hua, Rui Luo, Hui Jin

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virus evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
0.2field-weighted citation impact, top 47% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 1 institution in 1 country.

Bin MaState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Huimin GongState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Qianshuai XuState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Yuan GaoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Aohan GuanState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Haoyu WangState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Kexin HuaState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Rui LuoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.
Hui JinState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China.ORCID https://orcid.org/0000-0001-8004-2662
Huazhong Agricultural University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Understanding phylogenetic relationships among species is essential for many biological studies, which call for an accurate phylogenetic tree to understand major evolutionary transitions. The phylogenetic analyses present a major challenge in estimation accuracy and computational efficiency, especially recently facing a wave of severe emerging infectious disease outbreaks. Here, we introduced a novel, efficient framework called Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) for new sample placement for viruses. In this study, a brand-new recoding method called Frequency Vector Recoding was implemented to approximate the phylogenetic distance, and the Phylogenetic Simulated Annealing Search algorithm was developed to match the recoded distance matrix with the phylogenetic tree. Meanwhile, the indel (insertion/deletion) was heuristically introduced to foreign sequence recognition for the first time. Here, we compared the Bd-RPC with the recent placement software (PAGAN2, EPA-ng, TreeBeST) and evaluated it in

Indexed as

insertion/deletionnew sample placementphylogenetic treerecodingsimulated annealing

Identifiers

PMID38361823
PMCPMC10868571
OpenAlexW4391452453

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.