第一步 安装

conda install codonw
#使用conda命令安装codonw安装包并配置环境

第二步 使用

cd /home/monkeyflower/xiaodeng/codonw
#转到工作目录，要提前把需要分析的fasta文件放在这个目录下
codonw
#激活软件进入应用界面

Welcome to CodonW  for Help type h

 Initial Menu 
 Option
     (1) Load sequence file
     ( )
     (3) Change defaults
     (4) Codon usage indices
     (5) Correspondence analysis
     ( ) 
     (7) Teach yourself codon usage
     (8) Change the output written to file
     (9) About C-codons
     (R) Run C-codons 
     (Q) Quit 
 Select a menu choice, (Q)uit or (H)elp -> 

第一个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入4并回车。

 Codon usage indices
 Options
 ( 1)  Codon Adaptation Index       (CAI) 密码子适应指数
 ( 2)  Frequency of OPtimal codons  (Fop) 最优密码子使用频率
 ( 3)  Codon bias index             (CBI) 密码子偏好指数
 ( 4)  Effective Number of Codons   (ENc) 有效密码子数
 ( 5)  GC content of gene           (G+C) 基因的GC含量
 ( 6)  GC of silent 3rd codon posit.(GC3s) 密码子第三位点的GC含量
 ( 7)  Silent base composition 沉默base含量
 ( 8)  Number of synonymous codons  (L_sym) 同义密码子数目
 ( 9)  Total number of amino acids  (L_aa ) 氨基酸数目
 (10)  Hydrophobicity of protein    (Hydro) 蛋白质疏水性
 (11)  Aromaticity of protein       (Aromo) 蛋白质芳香性
 (12)  Select all 
 (X)  Return to previous menu
Choices enclosed with curly brackets are the current selections
 Select a menu choice, (Q)uit or (H)elp -> 

第二个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入12，输入12表示选中了所有分析项目，并回车

Codon usage indices
 Options
 ( 1) {Codon Adaptation Index       (CAI)           }
 ( 2) {Frequency of OPtimal codons  (Fop)           }
 ( 3) {Codon bias index             (CBI)           }
 ( 4) {Effective Number of Codons   (ENc)           }
 ( 5) {GC content of gene           (G+C)           }
 ( 6) {GC of silent 3rd codon posit.(GC3s)          }
 ( 7) {Silent base composition                      }
 ( 8) {Number of synonymous codons  (L_sym)         }
 ( 9) {Total number of amino acids  (L_aa )         }
 (10) {Hydrophobicity of protein    (Hydro)         }
 (11) {Aromaticity of protein       (Aromo)         }
 (12)  Select all 
 (X)  Return to previous menu
Choices enclosed with curly brackets are the current selections
 Select a menu choice, (Q)uit or (H)elp ->

第三个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入X并回车。

 Initial Menu 
 Option
     (1) Load sequence file
     ( )
     (3) Change defaults
     (4) Codon usage indices
     (5) Correspondence analysis
     ( ) 
     (7) Teach yourself codon usage
     (8) Change the output written to file
     (9) About C-codons
     (R) Run C-codons 
     (Q) Quit 
 Select a menu choice, (Q)uit or (H)elp ->

第四个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入1并回车

Loading sequence menu (type h for help)
 No sequence file is currently loaded

Name of input sequence file  (h for help) [input.dat] 

第五个界面有如上信息，在Name of input sequence file (h for help) [input.dat] 后输入所要检测的fasta文件名并回车，接着会弹出Name of output sequence file (h for help) [Camellia_minima.out] 和Name of bulk output file (h for help) [Camellia_minima.blk]，都直接回车就可以。

Initial Menu 
 Option
     (1) Load sequence file
     ( )
     (3) Change defaults
     (4) Codon usage indices
     (5) Correspondence analysis
     ( ) 
     (7) Teach yourself codon usage
     (8) Change the output written to file
     (9) About C-codons
     (R) Run C-codons 
     (Q) Quit 
 Select a menu choice, (Q)uit or (H)elp ->

第六个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入R并回车，后面会弹出一系列信息，直接回车就行。

Press return or enter to continue -> 

 Welcome to CodonW  for Help type h

 Initial Menu 
 Option
     (1) Load sequence file
     ( )
     (3) Change defaults
     (4) Codon usage indices
     (5) Correspondence analysis
     ( ) 
     (7) Teach yourself codon usage
     (8) Change the output written to file
     (9) About C-codons
     (R) Run C-codons 
     (Q) Quit 
 Select a menu choice, (Q)uit or (H)elp ->

第七个界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后输入Q并回车,一定不能忘记，否则数据不会保存。

分析完成