IHB OpenIR  > 鱼类生物学及渔业生物技术研究中心  > 期刊论文
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
Zhang, Dong1,2,3; Gao, Fangluan4; Jakovlic, Ivan5; Zou, Hong1,2; Zhang, Jin5; Li, Wen X.1,2; Wang, Gui T.1,2
2020
Source PublicationMOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
Volume20Issue:1Pages:348-355
Abstract

Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.

Keywordbatch capacity GenBank extraction high efficiency multicore operation partition analysis phylogenetic flowchart
DOI10.1111/1755-0998.13096
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000494565200001
WOS KeywordSOFTWARE ; ANNOTATION ; SELECTION ; MAFFT ; TREE ; TOOL
PublisherWILEY
Citation statistics
Cited Times:65[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/34998
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorLi, Wen X.; Wang, Gui T.
Affiliation1.Minist Agr, Key Lab Aquaculture Dis Control, Wuhan, Hubei, Peoples R China
2.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Hubei, Peoples R China
3.Univ Chinese Acad Sci, Beijing, Peoples R China
4.Fujian Agr & Forestry Univ, Inst Plant Virol, Fuzhou, Fujian, Peoples R China
5.Biotransduct Lab, Wuhan, Hubei, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Dong,Gao, Fangluan,Jakovlic, Ivan,et al. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies[J]. MOLECULAR ECOLOGY RESOURCES,2020,20(1):348-355.
APA Zhang, Dong.,Gao, Fangluan.,Jakovlic, Ivan.,Zou, Hong.,Zhang, Jin.,...&Wang, Gui T..(2020).PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.MOLECULAR ECOLOGY RESOURCES,20(1),348-355.
MLA Zhang, Dong,et al."PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies".MOLECULAR ECOLOGY RESOURCES 20.1(2020):348-355.
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