mse |
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% mse dna.msf msf::mse.msf Multiple Sequence Editor |
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Multiple Sequence Editor Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset File containing a sequence alignment [-outseq] seqoutset [ |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-sequence] (Parameter 1) |
seqset | File containing a sequence alignment | Readable set of sequences | Required |
[-outseq] (Parameter 2) |
seqoutset | Sequence set filename and optional format (output USA) | Writeable sequences | <*>.format |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-gcgmode | boolean | Use GCG Unix mode for keyboard shortcuts and commands | Boolean value Yes/No | No |
-protein | boolean | Sequences are protein | Boolean value Yes/No | $(acdprotein) |
Associated qualifiers | ||||
"-sequence" associated seqset qualifiers | ||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |
-sid1 -sid_sequence |
string | Entryname | Any string | |
-ufo1 -ufo_sequence |
string | UFO features | Any string | |
-fformat1 -fformat_sequence |
string | Features format | Any string | |
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
"-outseq" associated seqoutset qualifiers | ||||
-osformat2 -osformat_outseq |
string | Output seq format | Any string | |
-osextension2 -osextension_outseq |
string | File name extension | Any string | |
-osname2 -osname_outseq |
string | Base file name | Any string | |
-osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |
-osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |
-ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
-oufo2 -oufo_outseq |
string | UFO features | Any string | |
-offormat2 -offormat_outseq |
string | Features format | Any string | |
-ofname2 -ofname_outseq |
string | Features file name | Any string | |
-ofdirectory2 -ofdirectory_outseq |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
!!NA_MULTIPLE_ALIGNMENT dna.msf MSF: 120 Type: N January 01, 1776 12:00 Check: 3196 .. Name: MSFM1 Len: 120 Check: 8587 Weight: 1.00 Name: MSFM2 Len: 120 Check: 6178 Weight: 1.00 Name: MSFM3 Len: 120 Check: 8431 Weight: 1.00 // MSFM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC MSFM2 ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC MSFM3 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG MSFM1 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT MSFM2 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT MSFM3 TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT MSFM1 ACGTACGTAC GTACGTACGT MSFM2 ACGTACGTTG CAACGTACGT MSFM3 ACGTACGTAC GTACGTACGT |
!!NA_MULTIPLE_ALIGNMENT 1.0 mse.msf MSF: 120 Type: N 15/07/10 CompCheck: 2784 .. Name: MSFM1 Len: 120 Check: 8587 Weight: 1.00 Name: MSFM2 Len: 120 Check: 5766 Weight: 1.00 Name: MSFM3 Len: 120 Check: 8431 Weight: 1.00 // 1 50 MSFM1 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC MSFM2 ACGTACGTACGTACGTACGTacgt....ACGTACGTACGTACGTACGTAC MSFM3 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTCGTACGTACG 51 100 MSFM1 GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT MSFM2 GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT MSFM3 TACGTACGTACGTACGTACGTACGTACGTAACGTACGTACGTACGTACGT 101 120 MSFM1 ACGTACGTACGTACGTACGT MSFM2 ACGTACGTTGCAACGTACGT MSFM3 ACGTACGTACGTACGTACGT |
Program name | Description |
---|---|
edialign | Local multiple alignment of sequences |
emma | Multiple sequence alignment (ClustalW wrapper) |
eomega | Multiple sequence alignment (ClustalO wrapper) |
eomegapp | Profile with profile (ClustalO wrapper) |
eomegash | Sequence with HMM (ClustalO wrapper) |
eomegasp | Sequence with profile (ClustalO wrapper) |
infoalign | Display basic information about a multiple sequence alignment |
plotcon | Plot conservation of a sequence alignment |
prettyplot | Draw a sequence alignment with pretty formatting |
showalign | Display a multiple sequence alignment in pretty format |
tranalign | Generate an alignment of nucleic coding regions from aligned proteins |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.