第一步 安裝

conda install codonw
#使用conda命令安裝codonw安裝包并配置環(huán)境

第二步 使用

cd /home/monkeyflower/xiaodeng/codonw
#轉(zhuǎn)到工作目錄，要提前把需要分析的fasta文件放在這個目錄下
codonw
#激活軟件進入應(yīng)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 -> 

第一個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入4并回車。

 Codon usage indices
 Options
 ( 1)  Codon Adaptation Index       (CAI) 密碼子適應(yīng)指數(shù)
 ( 2)  Frequency of OPtimal codons  (Fop) 最優(yōu)密碼子使用頻率
 ( 3)  Codon bias index             (CBI) 密碼子偏好指數(shù)
 ( 4)  Effective Number of Codons   (ENc) 有效密碼子數(shù)
 ( 5)  GC content of gene           (G+C) 基因的GC含量
 ( 6)  GC of silent 3rd codon posit.(GC3s) 密碼子第三位點的GC含量
 ( 7)  Silent base composition 沉默base含量
 ( 8)  Number of synonymous codons  (L_sym) 同義密碼子數(shù)目
 ( 9)  Total number of amino acids  (L_aa ) 氨基酸數(shù)目
 (10)  Hydrophobicity of protein    (Hydro) 蛋白質(zhì)疏水性
 (11)  Aromaticity of protein       (Aromo) 蛋白質(zhì)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 -> 

第二個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入12，輸入12表示選中了所有分析項目，并回車

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 ->

第三個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入X并回車。

 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 ->

第四個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入1并回車

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

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

第五個界面有如上信息，在Name of input sequence file (h for help) [input.dat] 后輸入所要檢測的fasta文件名并回車，接著會彈出Name of output sequence file (h for help) [Camellia_minima.out] 和Name of bulk output file (h for help) [Camellia_minima.blk]，都直接回車就可以。

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 ->

第六個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入R并回車，后面會彈出一系列信息，直接回車就行。

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 ->

第七個界面有如上信息，在Select a menu choice, (Q)uit or (H)elp -> 后輸入Q并回車,一定不能忘記，否則數(shù)據(jù)不會保存。

分析完成