TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chengjie Chen; Hao Chen; Yi Zhang; Hannah Rae Thomas; Margaret H. Frank; Yehua He; Rui Xia

doi:10.1016/j.molp.2020.06.009

Molecular PlantJun 23, 2020BioinformaticsPeer-reviewed journal article

TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chengjie Chen iD, Hao Chen iD, Yi Zhang iD, Hannah Rae Thomas iD, Margaret H. Frank iD, Yehua He iD, Rui Xia iD

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Abstract

The rapid development of high-throughput sequencing (HTS) 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 user-friendly interface. The toolkit incorporates over 100 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, with a new plotting engine ("JIGplot") developed to maximum their interactive ability, which allows quick point-and-click modification to almost every graphic feature. TBtools is a 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.

In-depth summary

Claude Opus 5.5 · xhigh effort · 17 Oct 2026 · from the full text of version 3 (9 Mar 2020) · CC BY-NC-ND 4.0

Stand-alone, point-and-click Java toolkit bundling over 100 sequence, BLAST, GO/KEGG enrichment and interactive plotting functions, so wet-lab biologists can analyse sequencing-scale data without the command line.

Most bioinformatics tools are scripts in assorted languages that need command-line skills, which keeps many wet-lab biologists from analysing their own high-throughput sequencing data. TBtools puts routine analyses into one cross-platform graphical program and adds a plotting engine whose figures stay editable instead of being fixed images.

Key results

ClaimedTBtools gathers more than 100 functions into one stand-alone graphical program for Windows, Macintosh and Unix, replacing sequential command-line tool chains with point-and-click workflows.
Needs Java Runtime Environment 1.6 or newer; every panel follows the same pattern (choose input, choose output, press start). The paper's example task, extracting a gene family, otherwise needs gffread (Unix-only), BLAST and seqkit or custom scripts. No usability study, timing or accuracy comparison is reported. · Abstract; Developed for wet-lab biologists; Developed as an integrative toolkit
ClaimedFunctions cover sequence handling, a local BLAST wrapper, Gene Ontology (GO) and KEGG enrichment, plotting, and utilities such as big-file preview, phylogenetic tree editing and Ka/Ks calculation, organised in five menus.
Five catalogs: Sequence Toolkits (extraction, format conversion, open reading frame prediction), BLAST, GO&KEGG (enrichment, bar plots, gene extraction per term), Graphics (Venn diagrams, heatmaps, Circos graphs, eFP figures) and Others. The enrichment statistics and BLAST settings are not described. · Developed as an integrative toolkit; Function outline
ClaimedJIGplot, a new Java interactive graphics engine, keeps nearly every plot element editable by clicking, lets panels such as trees, alignments, gene structures and heatmaps be combined, and can switch cartesian to polar coordinates for circular layouts.
Graphs export as high-resolution bitmap or vector files. The features are described in prose only; no figures or comparison with other plotting software appear in this text. · Abstract; Developed to interactively present data
ClaimedThe authors report wide uptake: a large stable user base, outputs used in many published papers, and a set of heavily used functions refined through user feedback.
More than 15,000 stable users over five years and use in hundreds of peer-reviewed publications; frequently used functions include eFP Browser, Interactive Heatmap, Simple Circos and Gene Family Tool. No source, survey method or citation list is given for these figures. · Developed as an integrative toolkit; Stellar functions; Conclusion

Methods, data and reproducibility

A stand-alone Java desktop application with a graphical interface in which each function takes input and output paths and runs on a click; most functions are coded from scratch in Java, some call cross-platform programs such as BLAST, and graphs are drawn with the new JIGplot engine.

Methods & tools: TBtools, JIGplot, BLAST, Java Runtime Environment (1.6 or newer)
Reagents & environment: Java Runtime Environment 1.6 or newer on Windows, Macintosh or Unix.
Reproducibility gaps: The abstract says TBtools is free for non-commercial users, but the download link is missing from this text. Source code availability is not mentioned, and no example datasets are provided.

Limitations (4)

Most of the popular functions were not invented in TBtools; the authors describe them as optimised and simplified versions of existing tools. · stated by the authors
Free use is limited to non-commercial users. · stated by the authors
No benchmarks: correctness, speed and memory use on large files are not compared with the command-line tools TBtools replaces, and the algorithms behind enrichment, BLAST settings and Ka/Ks are not described. · noted in this summary
Adoption figures and the statement that tens of thousands of users have validated its robustness are given without supporting data or citations. · noted in this summary

Read this if you support wet-lab biologists who need point-and-click sequence handling, local BLAST, GO/KEGG enrichment or editable publication figures without scripting.