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needlerunner |
Standard (Mandatory) qualifiers: [-seqpairsdir] dirlist Input directory of files containing sequence pairs for alignment [-pathtocommand] directory Directory where alignment executable lives [-commandname] string Name of alignment executable [-scoringmatrixdirname] directory Directory where scoring matrix lives [-scoringmatrixname] string Name of alignment scoring matrix -gapopen float The gap opening penalty is subtracted from the total score every time a gap is inserted in the alignment. The default value is chosen for the EBLOSUM62 scoring matrix when you are aligning protein sequences, and the EDNAFULL matrix when you are aligning nucleotide sequences. If you sequence contains many small errors you should set a low gap opening penalty (near zero) to avoid over-penalizing those errors. -gapextend float The gap extension penalty is the score substracted when more spaces are added to an existing alignment gap. Often a single insertion or deletion affects multiple residues/nucleotides; separate opening and extension penalties reduce the excessive penalty such events would otherwise carry; generally the gap extension penalty should be significantly lower than the gap opening penalty. [-alignedseqsoutdir] outdir Name of directory containing sequences aligned by needle [-outfilesuffix] string Appended to end of all output alignment file names [-outfileformat] string Format of output alignments 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 |
scorer | Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment |
scorerrunner | Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third |
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 |