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scorerrunner |
Standard (Mandatory) qualifiers: [-pathtocommand] directory Directory where alignment executables live [-goldseqsdirlist] dirlist First directory containing paired traces [-testseqsdirlist] dirlist Second directory containing paired traces [-scoresoutdir] outdir Name of directory containing output scores [-scoresoutfilename] string Name of comma-separated variable file containing identity scores for pairs of gold and test sequences directory Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: (none) 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 |
Program name | Description |
---|---|
alignrunner | Runs alignment program on all sequence pairs in a directory |
contactalign | EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm |
esim4 | Align an mRNA to a genomic DNA sequence |
est2genome | Align EST and genomic DNA sequences |
nawalign | Damian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm |
nawalignrunner | Runs nawalign alignment program on all sequence pairs in a directory |
needle | Needleman-Wunsch global alignment |
needlerunner | Runs needle alignment program on all sequence pairs in a directory |
scorer | Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment |
stretcher | Finds the best global alignment between two sequences |
substitute | Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence) |
substituterunner | Runs substitute on directory of traces and writes substituted sequences to another |