Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and referenc...Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.展开更多
The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challen...The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.展开更多
基金supported by the Key Area Research and Development Program of Guangdong Province(2022B0202070003,and 2021B0707010004)supported by the National Science Foundation of China(#32072547,and#32102320)+5 种基金the National Key Research and Development Program(2021YFF1000101,and 2019YFD1000500)the Special Support Program of Guangdong Province(2019TX05N193)the Scientific Research Foundation of the Hunan Provincial Education Department(20A261),)the open competition program of top ten critical priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG05)C.C.is supported by the Guangzhou Municipal Science and Technology Plan Project(2023A04J0113)J.F.is supported by the Hainan Provincial Natural Science Foundation of China(323QN279).
文摘Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.
基金This work was funded by the National Key Research and Developmental Program of China(2018YFD1000104)This work is also supported by awards to R.X.,Y.H.,and H.C.from the National Key Research and Developmental Program of China(2017YFD0101702,2018YFD1000500,2019YFD1000500)+4 种基金the National Science Foundation of China(#31872063)the Special Support Program of Guangdong Province(2019TX05N193)the Key-Area Research and Development Program of Guangdong Province(2018B020202011)the Guangzhou Science and Technology Key Project(201804020063)Support to M.H.F.comes from the NSF Faculty Early Career Development Program(IOS-1942437).
文摘The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.