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alignrunner |
Standard (Mandatory) qualifiers: [-seqpairsdir] dirlist Input directory of files containing sequence pairs for alignment [-firstcommandpath] directory Directory where conventional alignment executable lives [-secondcommandpath] directory Directory where structure-weighted alignment executable lives [-firstcommandname] string Name of conventional alignment executable [-secondcommandname] string Name of structure-weighted alignment executable [-scoringmatrixdir] directory Directory where conventional scoring matrix lives [-scoringmatrixname] string Name of 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. -zeroend boolean If this option is true then no penalty is added for gaps at either ends of a trace. [-firstalignedseqsoutdir] outdir Name of directory containing sequences aligned by first method [-secondalignedseqsoutdir] outdir Name of directory containing sequences aligned by second method [-firstoutfilesuffix] string Appended to end of all output file names of sequences aligned by first alignment method [-secondoutfilesuffix] string Appended to end of all output file names of sequences aligned by second alignment method [-outfileformat] string Format of output alignments for both methods 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 |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqpairsdir] (Parameter 1) |
Input directory of files containing sequence pairs for alignment | Directory with files | . |
[-firstcommandpath] (Parameter 2) |
Directory where conventional alignment executable lives | Directory | |
[-secondcommandpath] (Parameter 3) |
Directory where structure-weighted alignment executable lives | Directory | |
[-firstcommandname] (Parameter 4) |
Name of conventional alignment executable | Any string is accepted | An empty string is accepted |
[-secondcommandname] (Parameter 5) |
Name of structure-weighted alignment executable | Any string is accepted | An empty string is accepted |
[-scoringmatrixdir] (Parameter 6) |
Directory where conventional scoring matrix lives | Directory | |
[-scoringmatrixname] (Parameter 7) |
Name of scoring matrix | Any string is accepted | An empty string is accepted |
-gapopen | 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. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence |
-gapextend | 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. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence |
-zeroend | If this option is true then no penalty is added for gaps at either ends of a trace. | Boolean value Yes/No | No |
[-firstalignedseqsoutdir] (Parameter 8) |
Name of directory containing sequences aligned by first method | Output directory | |
[-secondalignedseqsoutdir] (Parameter 9) |
Name of directory containing sequences aligned by second method | Output directory | |
[-firstoutfilesuffix] (Parameter 10) |
Appended to end of all output file names of sequences aligned by first alignment method | Any string is accepted | An empty string is accepted |
[-secondoutfilesuffix] (Parameter 11) |
Appended to end of all output file names of sequences aligned by second alignment method | Any string is accepted | An empty string is accepted |
[-outfileformat] (Parameter 12) |
Format of output alignments for both methods | Any string is accepted | fasta |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
Under development, no example input file(s) yet
Under development, no example output file(s) yet
Program name | Description |
---|---|
comparator | Compare contact scores of two sequence alignments |
contactalign | Damian Counsell's experimental 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 NW implementation |
nawalignrunner | Nawalign all sequence pairs in a directory |
needle | Needleman-Wunsch global alignment |
needlerunner | Needle all sequence pairs in a directory |
scorer | Score alignments using structural alignments |
scorerrunner | SCORER for ordered pairs of substituted seqs |
stretcher | Finds the best global alignment between two sequences |
substitute | Substitute matches into a template |
substituterunner | Run SUBSTITUTE on a directory of traces |