EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BMC Bioinformatics

Software

Yuqin Zhang¹  Dao-Feng Zhang²  Zhe Zhao²  Wei He²  Zongze Shao³  Wen-Jun Li⁴  Iftikhar Ahmed⁵ 

[1] Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, 100050, Beijing, China;Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, 210098, Nanjing, China;Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, 210098, Nanjing, China;Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, China;Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, 210098, Nanjing, China;State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China;National Agricultural Research Centre (NARC), Land Resources Research Institute (LRRI), National Culture Collection of Pakistan (NCCP), 45500, Islamabad, Pakistan;

关键词: Phylogeny inference;    Supermatrix;    Supertree;    Prokaryote taxonomy;    Core gene;   

DOI  :  10.1186/s12859-023-05527-2

 received in 2023-05-06, accepted in 2023-10-10,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundGenome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches.ResultsEasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines.ConclusionsEasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4).

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

Fig. 5