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substituterunner |
Standard (Mandatory) qualifiers:
[-commandpath] directory Directory where alignment executables live
[-alignedpairsdir] dirlist Directory containing paired traces
[-substitutedseqsoutdir] outdir Directory to write substituted sequences to
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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-commandpath] (Parameter 1) |
Directory where alignment executables live | Directory | |
| [-alignedpairsdir] (Parameter 2) |
Directory containing paired traces | Directory with files | . |
| [-substitutedseqsoutdir] (Parameter 3) |
Directory to write substituted sequences to | Output directory | |
| 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 |
|---|---|
| alignrunner | Align sequence pairs in a directory |
| 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 |