ITEP: An integrated toolkit for exploration of microbial pan-genomes
没有git的先安装git：
sudo apt-get install git
下载ITEP：
git clone git@github.com:mattb112885/clusterDbAnalysis
Verifying permissions：
cd clusterDbAnalysis
sudo chmod u+x src/*.py
sudo chmod u+x src/*.sh
sudo chmod u+x src/internal/*.py
sudo chmod u+x src/internal/*.sh
sudo chmod u+x src/utilities/*.py
sudo chmod u+x src/utilities/*.sh
sudo chmod u+x scripts/*.py
sudo chmod u+x scripts/*.sh
设置环境变量：
vim ~/.bashrc
i
source $HOME/tools/ITEP/clusterDbAnalysis/SourceMe.sh#具体按照自己的目录来写
按ESC键
shift + :
wq!
source ~/.bashrc
依赖包检查：
进入软件目录，运行检查命令，会列出未安装的依赖包，然后依次安装即可：
cd clusterDbAnalysis
./checkForDependencies.sh
比较难安装的依赖包：
sudo add-apt-repository ppa:bitcoin/bitcoin
sudo apt-get update
sudo apt-get install -y libdb4.8-dev libdb4.8++-dev
sudo dpkg -i libwxbase2.8-0_2.8.12.1+dfsg2-2ubuntu2+1_webupd8_xenial0_amd64.deb
sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb
sudo dpkg -i libwxgtk2.8-0_2.8.12.1+dfsg2-2ubuntu2+1_webupd8_xenial0_amd64.deb
myrast
sudo dpkg -i myrast-runtime_1.0-1ubuntu1_amd64.deb
sudo dpkg -i myrast_33-1ubuntu2_amd64.deb
二、使用
1. 运行前首先要在软件目录下运行如下命令：
source SourceMe.sh
2. 导入数据
需要genebank格式的文件
4. 建立ITEP数据库
建立数据库1-BLASTP and BLASTN
建立数据库2-MCL Clustering
建立数据库2-将来自其他cluster方法的结果导入ITEP
建立数据库3-Contig import
建立数据库4-RPSBLAST
5. 比较基因组分析
（1）Entry points into the database (read this first!)
（2）Searching for genes by gene properties
（3）Searching for genes by homology with other genes
（4）Obtaining information about genes
（5）Obtaining the complete sequences of contigs, genes or proteins
（6）Extracting DNA and amino acid sequences from a region of a genome, gene or protein
（7）Building alignments and trees
（8）Analyzing gene neighborhoods
（9）Searching for gene families by presence and absence patterns
（10）Visualizing homology patterns
（11）Building a concatinated gene tree
（12）Generating draft metabolic reconstructions from a reference
（13）Searching for missing genes and identifying causes for absence with tBLASTn
（14）Identifying the upstream regions of homologous proteins
（15）Searching for functions using conserved domains
（16）Adding user-defined gene data to ITEP
（17）Obtaining a list of bidirectional-best BLAST hits
（18）Turning ITEP IDs into human-readable formats
（19）Comparing the results of different clustering approaches
