|   | aligncopy | 
| % aligncopy Reads and writes alignments Input (aligned) sequence set: globins.msf Output alignment [globins.aligncopy]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing a sequence alignment.
  [-outfile]           align      [*.aligncopy] Output alignment file name
   Additional (Optional) qualifiers:
   -name               string     Name of the alignment (Any string is
                                  accepted)
   -comment            string     Comment on the alignment (Any string is
                                  accepted)
   -append             boolean    [N] This allows you to append the name and
                                  comments you have given on to the end of the
                                  existing alignment header.
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-sequences" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -aformat2           string     Alignment format
   -aextension2        string     File name extension
   -adirectory2        string     Output directory
   -aname2             string     Base file name
   -awidth2            integer    Alignment width
   -aaccshow2          boolean    Show accession number in the header
   -adesshow2          boolean    Show description in the header
   -ausashow2          boolean    Show the full USA in the alignment
   -aglobal2           boolean    Show the full sequence in alignment
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 | |
|---|---|---|---|
| [-sequences] (Parameter 1) | File containing a sequence alignment. | Readable set of sequences | Required | 
| [-outfile] (Parameter 2) | Output alignment file name | Alignment output file | <*>.aligncopy | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -name | Name of the alignment | Any string is accepted | An empty string is accepted | 
| -comment | Comment on the alignment | Any string is accepted | An empty string is accepted | 
| -append | This allows you to append the name and comments you have given on to the end of the existing alignment header. | Boolean value Yes/No | No | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 
!!AA_MULTIPLE_ALIGNMENT 1.0
  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..
  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43
//
           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD
           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN
           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA
           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~
 | 
The output is a standard EMBOSS alignment file.
The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences.
The available multiple alignment format names are: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
| 
########################################
# Program: aligncopy
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: aligncopy
#    -sequences ../../data/globins.msf
# Align_format: simple
# Report_file: globins.aligncopy
########################################
#=======================================
#
# Aligned_sequences: 7
# 1: HBB_HUMAN
# 2: HBB_HORSE
# 3: HBA_HUMAN
# 4: HBA_HORSE
# 5: MYG_PHYCA
# 6: GLB5_PETMA
# 7: LGB2_LUPLU
# Matrix: EBLOSUM62
#
# Length: 164
# Identity:       1/164 ( 0.6%)
# Similarity:    93/164 (56.7%)
# Gaps:          31/164 (18.9%)
# 
#
#=======================================
HBB_HUMAN          1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR     40
HBB_HORSE          1 --------VQLSGEEKAAVLALWDKVN-EEEVGGEALGR-LLVVYPWTQR     40
HBA_HUMAN          1 --------------VLSPADKTNVKAA-WGKVGAHAGEYGAEALERMFLS     35
HBA_HORSE          1 --------------VLSAADKTNVKAA-WSKVGGHAGEYGAEALERMFLG     35
MYG_PHYCA          1 -------VLSEGEWQLVLHVWAKVEAD-VAGHGQDILIR-LFKSHPETLE     41
GLB5_PETMA         1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE     50
LGB2_LUPLU         1 --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD     42
                               ::  : : :.: : : :   :::: ::   :  : :  : 
HBB_HUMAN         41 FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE     90
HBB_HORSE         41 FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE     90
HBA_HUMAN         36 FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD     85
HBA_HORSE         36 FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD     85
MYG_PHYCA         42 KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ     91
GLB5_PETMA        51 FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD    100
LGB2_LUPLU        43 LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN     92
                     :: ::  ::  : : :: ::: :::::: :: : : ::::::   : |::
HBB_HUMAN         91 LHCDKLH--VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA    138
HBB_HORSE         91 LHCDKLH--VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA    138
HBA_HUMAN         86 LHAHKLR--VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS    133
HBA_HORSE         86 LHAHKLR--VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS    133
MYG_PHYCA         92 SHATKHK--IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR    139
GLB5_PETMA       101 LSGKHAK--SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA    148
LGB2_LUPLU        93 LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA    142
                     ::: :::  ::: ::::: : :: ::: :   :::::: ::: : :: ::
HBB_HUMAN        139 NALAHKYH------    146
HBB_HORSE        139 NALAHKYH------    146
HBA_HUMAN        134 TVLTSKYR------    141
HBA_HORSE        134 TVLTSKYR------    141
MYG_PHYCA        140 KDIAAKYKELGYQG    153
GLB5_PETMA       149 Y-------------    149
LGB2_LUPLU       143 IVIKKEMNDAA---    153
                       :  ::       
#---------------------------------------
#---------------------------------------
 | 
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
| Program name | Description | 
|---|---|
| aligncopypair | Reads and writes pairs from alignments | 
| biosed | Replace or delete sequence sections | 
| codcopy | Copy and reformat a codon usage table | 
| cutseq | Removes a section from a sequence | 
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences | 
| descseq | Alter the name or description of a sequence | 
| entret | Retrieves sequence entries from flatfile databases and files | 
| extractalign | Extract regions from a sequence alignment | 
| extractfeat | Extract features from sequence(s) | 
| extractseq | Extract regions from a sequence | 
| featcopy | Reads and writes a feature table | 
| featreport | Reads and writes a feature table | 
| listor | Write a list file of the logical OR of two sets of sequences | 
| makenucseq | Create random nucleotide sequences | 
| makeprotseq | Create random protein sequences | 
| maskambignuc | Masks all ambiguity characters in nucleotide sequences with N | 
| maskambigprot | Masks all ambiguity characters in protein sequences with X | 
| maskfeat | Write a sequence with masked features | 
| maskseq | Write a sequence with masked regions | 
| newseq | Create a sequence file from a typed-in sequence | 
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file | 
| noreturn | Remove carriage return from ASCII files | 
| nospace | Remove all whitespace from an ASCII text file | 
| notab | Replace tabs with spaces in an ASCII text file | 
| notseq | Write to file a subset of an input stream of sequences | 
| nthseq | Write to file a single sequence from an input stream of sequences | 
| pasteseq | Insert one sequence into another | 
| revseq | Reverse and complement a nucleotide sequence | 
| seqret | Reads and writes (returns) sequences | 
| seqretsplit | Reads sequences and writes them to individual files | 
| sizeseq | Sort sequences by size | 
| skipredundant | Remove redundant sequences from an input set | 
| skipseq | Reads and writes (returns) sequences, skipping first few | 
| splitter | Split sequence(s) into smaller sequences | 
| trimest | Remove poly-A tails from nucleotide sequences | 
| trimseq | Remove unwanted characters from start and end of sequence(s) | 
| trimspace | Remove extra whitespace from an ASCII text file | 
| union | Concatenate multiple sequences into a single sequence | 
| vectorstrip | Removes vectors from the ends of nucleotide sequence(s) | 
| yank | Add a sequence reference (a full USA) to a list file |