|   | codcopy | 
| % codcopy Reads and writes a codon usage table Codon usage file: Eecoli.cut Codon usage output file [eecoli.cut]: | 
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-infile]            codon      Codon usage table name
  [-outfile]           outcodon   Codon usage table name
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-infile" associated qualifiers
   -format1            string     Data format
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Output format specific to this data type
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-infile] (Parameter 1) | Codon usage table name | Codon usage file in EMBOSS data path | |
| [-outfile] (Parameter 2) | Codon usage table name | Codon usage file | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| #Species: Escherichia coli K12 #Division: gbbct #Release: CUTG146 #CdsCount: 5045 #Coding GC 51.81% #1st letter GC 58.93% #2nd letter GC 40.69% #3rd letter GC 55.80% #Codon AA Fraction Frequency Number GCA A 0.214 20.299 32456 GCC A 0.269 25.493 40761 GCG A 0.355 33.631 53773 GCT A 0.162 15.354 24549 TGC C 0.554 6.431 10283 TGT C 0.446 5.180 8282 GAC D 0.372 19.047 30454 GAT D 0.628 32.219 51514 GAA E 0.690 39.570 63268 GAG E 0.310 17.782 28431 TTC F 0.425 16.580 26510 TTT F 0.575 22.423 35852 GGA G 0.108 7.925 12671 GGC G 0.402 29.403 47013 GGG G 0.150 10.994 17578 GGT G 0.340 24.838 39714 CAC H 0.429 9.712 15529 CAT H 0.571 12.903 20630 ATA I 0.072 4.290 6860 ATC I 0.419 24.999 39971 ATT I 0.510 30.427 48649 AAA K 0.767 33.618 53752 AAG K 0.233 10.198 16305 CTA L 0.036 3.860 6172 CTC L 0.104 11.045 17660 CTG L 0.496 52.821 84455 CTT L 0.104 11.051 17670 TTA L 0.131 13.913 22246 TTG L 0.129 13.727 21948 ATG M 1.000 27.778 44414 AAC N 0.551 21.611 34554 AAT N 0.449 17.633 28193 CCA P 0.192 8.524 13629 CCC P 0.125 5.531 8843 CCG P 0.524 23.235 37150 CCT P 0.159 7.045 11265 CAA Q 0.349 15.474 24742 CAG Q 0.651 28.832 46100 AGA R 0.037 2.056 3287 AGG R 0.022 1.216 1944 CGA R 0.064 3.542 5663 CGC R 0.398 22.005 35184 CGG R 0.098 5.391 8619 CGT R 0.381 21.020 33609 AGC S 0.277 16.031 25632 AGT S 0.151 8.723 13947 TCA S 0.123 7.137 11411 TCC S 0.148 8.591 13736 TCG S 0.154 8.916 14256 TCT S 0.147 8.507 13601 ACA T 0.131 7.035 11248 ACC T 0.435 23.362 37354 ACG T 0.268 14.371 22977 ACT T 0.166 8.922 14265 GTA V 0.154 10.883 17400 GTC V 0.215 15.221 24336 GTG V 0.371 26.253 41976 GTT V 0.260 18.394 29410 TGG W 1.000 15.303 24468 TAC Y 0.429 12.243 19576 TAT Y 0.571 16.326 26103 TAA * 0.642 2.025 3237 TAG * 0.072 0.228 365 TGA * 0.286 0.902 1443 | 
| Program name | Description | 
|---|---|
| biosed | Replace or delete sequence sections | 
| cutseq | Removes a specified section from a sequence | 
| degapseq | Removes gap characters from sequences | 
| descseq | Alter the name or description of a sequence | 
| entret | Reads and writes (returns) flatfile entries | 
| extractalign | Extract regions from a sequence alignment | 
| extractfeat | Extract features from a sequence | 
| extractseq | Extract regions from a sequence | 
| listor | Write a list file of the logical OR of two sets of sequences | 
| makenucseq | Creates random nucleotide sequences | 
| makeprotseq | Creates random protein sequences | 
| maskfeat | Mask off features of a sequence | 
| maskseq | Mask off regions of a sequence | 
| newseq | Type in a short new sequence | 
| noreturn | Removes carriage return from ASCII files | 
| notseq | Exclude a set of sequences and write out the remaining ones | 
| nthseq | Writes one sequence from a multiple set of sequences | 
| pasteseq | Insert one sequence into another | 
| revseq | Reverse and complement a sequence | 
| seqret | Reads and writes (returns) sequences | 
| seqretsplit | Reads and writes (returns) sequences in individual files | 
| skipseq | Reads and writes (returns) sequences, skipping first few | 
| splitter | Split a sequence into (overlapping) smaller sequences | 
| trimest | Trim poly-A tails off EST sequences | 
| trimseq | Trim ambiguous bits off the ends of sequences | 
| union | Reads sequence fragments and builds one sequence | 
| vectorstrip | Strips out DNA between a pair of vector sequences | 
| yank | Reads a sequence range, appends the full USA to a list file |