【3.1.2】clustalw

一、安装

wget -c http://www.clustal.org/download/current/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz
tar xvzf clustalw-2.1-linux-x86_64-libcppstatic.tar.gz

二、用法

cd /data/software/clustalw-2.1-linux-x86_64-libcppstatic
./clustalw2 -help

-INFILE=file.ext                             :input sequences.
-PROFILE1=file.ext  and  -PROFILE2=file.ext  :profiles (old alignment).


                VERBS (do things)

-OPTIONS            :list the command line parameters
-HELP  or -CHECK    :outline the command line params.
-FULLHELP           :output full help content.
-ALIGN              :do full multiple alignment.
-TREE               :calculate NJ tree.
-PIM                :output percent identity matrix (while calculating the tree)
-BOOTSTRAP(=n)      :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
-CONVERT            :output the input sequences in a different file format.

-TYPE=         :PROTEIN or DNA
./clustalw2 -help

三、使用案例

/data/software/clustalw-2.1-linux-x86_64-libcppstatic/clustalw2  -ALIGN -INFILE=./final_designs.fa -TYPE=DNA

生成文件：

final_designs.fa.aln  #比对结果
final_designs.fa.dnd #打分文件

参考资料

http://www.clustal.org/download/current/