/TBtools

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

Primary LanguageShellGNU General Public License v3.0GPL-3.0

Introduction

​ TBtools is a Toolset written by CJ-Chen for wet-lab biologists.

TBtools main panel

​ Up to now, it contains functions more than that listed HERE:


序列操作工具集,Sequence Toolkits ​

  • Fasta序列(含区段)提取,Amazing Fasta Extractor、Fasta Extractor和Fasta Subseq
  • Fasta序列合并和分割,Fasta Merge and Split
  • 序列格式化(序列反向、互补和按指定行宽分行),Sequence Manipulator
  • NCBI序列批量下载,NCBI Seq DownLoader
  • cDNA序列完成开放阅读框预测,Get Complete ORF
  • 序列库中引物特异性检测,Check Primers
  • gff3/gtf序列提取,Gtf/Gff3 Sequences Extractor

​ Blast界面化工具集,Blast

  • 调用NCBI API进行远程Blast,Remote Blast
  • 少量序列Blast比对到大序列库文件,Auto Blast SeveralSequences To a Big File
  • 少量序列比对到少量序列,Auto Blast TwoSequence Sets
  • 大序列库文件比对到大序列库文件,Auto Blast TwoSequence Sets -Big File-
  • 序列比对到Fastq文件,Blast Several Seq ToFastQ
  • 互惠Blast(用于不同序列库ID映射),Reciprocal Blast
  • 序列比对结果区段映射图绘制,Blast XML AlignmentShower
  • 序列比对结果点阵图绘制,Blast XMLDotplot
  • 序列比对结果堆叠图绘制,Blast XMLPileup Grapher
  • BlastXML结果转换为TBtools比对结果表格,TranFormat Blast .xml to TBtools.table
  • BlastXML结果转换为Blast表格结果,TranFormat Blast .xml to Blast Table
  • 基于测序数据的电子克隆,e-GenomeWalkingor e-Race

GeneOntology和KEGG工具集,GO and KEGG

  • GO注释,GO Anotation
  • GO富集,GO Enrichment
  • GO层级统计和绘制,GO Level Counter
  • GO层级比较,GO Level Compare
  • GO注释解析,GO Term Parser
  • GO注释转换为BiNGO输入结果,Prepare GO Annotaiton For BinGO in cytoscape
  • KEGG通路富集工具,KEGG Enrichment Analysis
  • KEGG****通路差异表达基因描图工具,KEGG Pathway Map Drawer

​ 其他工具集,Others ​

  • 取色器,Color Picker
  • 表格提取(行筛选),Table IDManipulator
  • 表格列操作(列排序和保留),Table ColumnManipulator
  • 大文本极速查看(支持.gz压缩格式),Big Text Viewer
  • 大表格极速查看(支持.gz压缩格式),Big Table Viewer
  • 基于标识符号提取文本区段,Text Block Extractor
  • 表达量快速查看/比较,Expression Shower
  • 读段计数做RPKM/FPKM/TPM标准化,Expression Calculator (RPKM/FPKM/TPM)
  • 2~6组可交互韦恩图绘制,Wonderful Venn (Up to Six Sets)
  • 基于序列在染色体上展示基因位置,Map Genes OnGenome From Sequence Files
  • 基于坐标在染色体上展示基因位置,Map Genes OnGenome From Position Info Files
  • 基因组共线性分析结果可视化,Dual SystenyPlotter for MCscanX

​ About工具,About

  • 默认界面(可直接拖拽.png/.jpg图片,输出Kmeans聚类色卡),About TBtools
  • debug对话框,Debug Dialog
  • 调整TBtools初始化内存,Resize JVMmemory


Compatability

​ It can run in all Operating system including Mac, Linux, Windows, which have Java run time environment higher than 1.6. Both command line usages and GUI manipulation have been implemented. U can use it and distribute it freely, for researches or for commecial purpose. Well, if u found it useful to u, I will be very graceful that u cite TBtools in u paper...

List of Supporters

  • Hao Chen from Hunan Agricultural University
  • Kun Lu from Southwest University

How to Cite TBtools

TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface

Dowload

Click to download the excutable .jar file

Current Version No.0.58

sci-hub available address sci-hub.bz