miemiemiem / tbtools Goto Github PK

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。

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

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

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

​

​ 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...

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

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

Click to download the excutable .jar file