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mse |
% mse dna.msf msf::mse.msf Multiple Sequence Editor |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-sequence] seqset File containing a sequence alignment [-outseq] seqoutset Output sequence set USA Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" 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 "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
File containing a sequence alignment | Readable set of sequences | Required |
[-outseq] (Parameter 2) |
Output sequence set USA | Writeable sequences | <sequence>.format |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
!!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 15/07/05 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 |
---|---|
emma | Multiple alignment program - interface to ClustalW program |
infoalign | Information on a multiple sequence alignment |
plotcon | Plot quality of conservation of a sequence alignment |
prettyplot | Displays aligned sequences, with colouring and boxing |
showalign | Displays a multiple sequence alignment |
tranalign | Align nucleic coding regions given the aligned proteins |