TBtools GitHub ReadMe

## Please Note:

**TBtools** is **ONLY** freely available for academic research. And for **commercial usage**, please contact me ([email protected])


TBtools对于学术研究以及学术培训（由学术机构开设的公益性质且不收费的培训）是免费的。对于其商业用途，请通过我的邮箱联系我。


Use TBtools for **fee-based Training** is included in "Commercial usage".


商业用途包括在收费的培训中使用TBtools。


## Introduction

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



![main.png](https://upload-images.jianshu.io/upload_images/10518391-9db1ed53904dec3c.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240)



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

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新增热门工具，

* **Amazing Heatmap Generator**热图工具
* **Amazing Gene Viewer**同时展示进化树，MEME结果和基因结果与结构域

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

​   

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## Compatability

​   It can run in all Operating system including Mac, Linux, Windows, which have [Java run time environment higher than 1.6](http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html).  Both **command line usages and GUI manipulation** have been implemented.  You can ONLY use it and distribute it **freely, for researches**. 
Well, if you found it useful, I will **be very graceful if you cite TBtools** in your 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](https://www.biorxiv.org/content/early/2018/03/27/289660)

### 0410  

## Dowload

[Click to download the excutable .jar file](https://github.com/CJ-Chen/TBtools/archive/master.zip)

https://mp.weixin.qq.com/s/4t6M1O1VXA9LVIH48iOegg
https://mp.weixin.qq.com/s/gnabh2Bd4PyaKPFg5fjdEQ
## Current Version No.1.047
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#### Ad Exempt:125.88.24.\d+
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## TBtools:Please update to the lastest version (higher than v1.045).
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