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mse |
Standard (Mandatory) qualifiers: [-sequence] seqset File containing a sequence alignment Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -tmpdir outdir Temp directory 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 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 |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
-tmpdir | Temp directory | Output directory | /tmp |
Program name | Description |
---|---|
emma | Multiple alignment program - interface to ClustalW program |
infoalign | Information on a multiple sequence alignment |
plotcon | Plots the 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 |