Alphabetic List of Delila Programs

  • alist: aligned listing of a book
  • alpro: frequency and information of aligned sequences
  • alword: frequency and information of aligned words
  • aran: aligned random sequences
  • asciicode: converts ascii table to Pascal code
  • asciidna: draw ASCII DNA
  • auxmod: modules for auxiliary programs
  • av: average integers
  • between: compute whether a number is between two other numbers
  • bigbuf: show last n characters of a file
  • biglet: text enlargement program
  • binom: produce the binomial probabilities for a found black to white ratio
  • binomial: produce the binomial probabilities for a found black to white ratio
  • binplo: produce the binomial probabilities for a found black to white ratio
  • biscan: multiple part scanning program
  • bk2seq: takes a book file and makes it a protseq file.
  • bkdb: convert a book to database format for the sites program
  • bndrec: create marks file for a boundrectangle
  • bookends: report the endpoint coordinates of pieces in a book
  • bookshift: shift the coordinates in a book according to an inst
  • calc: a calculator that propagates errors
  • calhnb: small-sample correction for information and uncertainty
  • calico: character and line counts of a file
  • cap: put capital letters inside quotes of a program
  • capsmark: read sequence; make features for capitalized regions
  • catal: cataloguer of delila libraries, the catalogue program
  • censor: removes code from a program
  • center: center text lines
  • cerf: complement of the error function
  • chacha: changes characters in a file
  • chaos: chaotic analysis of scan data
  • chi: estimates chi squared from degrees of freedom
  • cisq: circle to square
  • ckhelix: check that the helix location is where one wants
  • clual: clustal to alpro conversion
  • cluster: cluster indana subindexes into groups of duplicate entries
  • cnsr: removes text from a file
  • coda: composition file to data for genhis
  • codecomments: find the comment density of a pascal program
  • column: pull defined column from input
  • comp: determine the composition of a book.
  • compan: composition analysis.
  • concat: concatenate files together
  • consensus: convert symvec to consensus to point out flaws in consensus
  • coscurve: compute the length of the cosine curve
  • count: count the amount of sequence in a Delila system book
  • counter: program counter
  • csvtospace: convert a comma delimited csv file to a space delimeted file
  • cumulative: cumulative probability distribution
  • curvafea: DNA curvature to lister features
  • cutoff: cutoff scan data
  • da3d: diana da file to 3d graphics
  • da3drotate: da3drotate the da3dp scene
  • dalvec: converts Rseq rsdata file to symvec format
  • dangles: dangles: DNA angles
  • dashseq: convert aligned sequences with dashes to pure sequences
  • datarange: limit the range of a data table
  • dbbk: database to delila book conversion program
  • dbcat: database catalog production and sorting program.
  • dbclean: remove non-entry material
  • dbfilter: filter GenBank databases to remove unwanted entries
  • dbinst: extract Delila instructions from a GenBank database
  • dblo: look at the catalogue of a genbank/embl database
  • dbmutate: mutate genbank database
  • dbpull: database extraction program.
  • decat: break a file into 10 files
  • decimals: determine the number of decimal places in a real number
  • decom: remove comments from within a comment
  • dehtml: remove html structures
  • delila: the librarian for sequence manipulation
  • delmod: delila module library
  • denav: density average
  • denplo: density plot in color
  • denri: compute density for delta Ri
  • derivative: take the derivative of x versus y in xyin
  • derive: compute the derivative curve for a xyin
  • diana: dinucleotide analysis of an aligned book
  • diffinst: find the difference between all coordinates in two inst files
  • diffint: differences between integers
  • diffintcut: differences between integers with cutoff
  • diffribl: calculate the difference between two ribls
  • difri: difference in Ri values in a scan data file
  • digrab: diagonal grabs of diana data
  • dirgra: directed graph Monte Carlo analysis
  • diri: finds the information for all sites in a flex model
  • dirty: calculate probabilities for dirty DNA synthesis
  • discan: combine two feature files into one model
  • disum: distance vs Ri sum
  • dnag: graphics of DNA
  • dnamwt: calculate the molecular weight of a DNA molecule
  • dnaplot: plot Ri values for one or more large DNA sequences
  • domod: doodle modules
  • doodle: pascal graphics library and preprocessor for pic under unix
  • dops: pascal graphics library and preprocessor for postscript
  • dosun: pascal graphics library and preprocessor for Sun graphics
  • dotmat: dot matrices of two books
  • dotsba: dots to database
  • doudiff: double differences between integers
  • embed: embed an aligned set of DNA sequences into random sequences
  • emin: E theoretical curve
  • emptytest: Test for file empty
  • encfrq: encoded sequence frequency analysis
  • encode: encodes a book of sequences into strings of integers
  • encsum: sum of the vectors of encoded sequences
  • epsclean: clean an eps file
  • ev: evolution of binding sites
  • evd: evolution display
  • exon: determine lengths of exons in GenBank entries
  • expgraph: make a graph of the exponential function
  • exponential: create an exponential curve for binding site separtions
  • exponentmax: determine the largest argument of the exp() function
  • fastcat: create a Delila catalogue very quickly
  • fdr: computes best values of sigma/D for f_D(r) fit of real data.
  • fico: find control characters in the input file
  • fileposition: report the line that has a given file position
  • fitgauss: fit a gaussian distribution to a histogram
  • fl: points out excessively long lines
  • flag: points out excessively long lines
  • flag78: points out excessively long lines
  • frag: create delila instructions to grab fragments from a book
  • frame: evaluator of potential reading frames
  • freb: frequency table to Delila book
  • frese: frequency table to sequ
  • fv: flip lines of a file vertically
  • gap: gaps in aligned listing of a book
  • gauss: generate a bunch of gaussianly distributed numbers
  • gaussint: creates a table of values representing the integral of the gaussian
  • genhis: general histogram plotter
  • genmod: genbank access modules
  • genpic: convert genhis output to pic input
  • gentst: test random generator
  • gifnormalize: normalize a gif file to a given size
  • gpctime: test time for the gpc compiler
  • helix: find helices between sequences in two books
  • helixside: distances converted to DNA helical angle.
  • helloworld: a minimal Pascal program to test that your compiler works
  • hgraph: make uncertainty (H) graph
  • hist: make a histogram of aligned sequences.
  • histan: histogram analysis.
  • htmlink: insert html links to program references in a file
  • httplink: find URLs in a file and make them into links
  • ic: inches to cm
  • imgalt: html image alt detection and upgrading for 508 requirements
  • indana: analysis of an index
  • index: make an alphabetic list of oligonucleotides in a book
  • instal: delila instruction alignment
  • instshift: shift coordinates of delila instructions
  • kenin: create Delila instructions from Ken's all.gen instructions
  • keymat: keyed-matrices for helices between two books
  • lenin: convert a list of lengths into Delila instructions
  • lidel: convert coordinate list to Delila instructions
  • lig: DNA ligation theory
  • linreg: linear regression
  • lister: list the sequences in a book with translation and sequence walkers
  • live: LIster waVEs
  • ll: line lengths
  • localbest: find features with the highest Ri in a given sequence range
  • lochas: look at characters in a file
  • log: compute log of a data column
  • logav: log average
  • logscale: provide numbers on a log scale
  • loocat: look at a catalogue
  • makebk: make a book from a file of sequences.
  • makegauss: make a gaussian distribution from a histogram
  • makeinst: generate delila instructions for set A and B from dcout.
  • makelogo: make a graphical `sequence logo' for aligned sequences
  • makewalker: walk an information weight matrix across a sequence
  • makman: make manual entries from a source code
  • makmod: create a set of empty modules from a list of names
  • maknam: make manual entry names
  • malign: optimal alignment of a book, based on minimum uncertainty
  • malin: make delila instructions from nth alignment of malign
  • malopt: 2d plot of optimal alignments
  • markov: markov chain generation of a DNA sequence from composition.
  • matmod: mathematics modules
  • matrix: dot matrices for helices between two books
  • medlinebib: convert medline Unix query format to bibtex format
  • memory: analysis of computer memory
  • merge: compare two files and merge them
  • mergemarks: merge lister marks files
  • meri: merge ribl files
  • mfoldfea: convert mfold RNA structure to lister feature
  • mfoldseq: make seq file for the mfold program
  • migrate: selective migration of drunkard's walk
  • mkdb: read sequence; make GenBank entry with features for capitalized regions
  • mkdis: define a distribution
  • mnomial: produce the multinomial distribution for base probabilities
  • modin: generate modularized delila instructions for absolute sites
  • modlen: determine module lengths
  • module: module replacement program
  • mstrip: remove control m's from a file
  • multiscan: scan a book for many linked binding sites
  • multtest: multiple Student's t-test
  • mutseq: mutate a sequence
  • noblank: remove all blank lines from a file
  • nocom: remove comments from a program
  • nohigh: no high order characters in output
  • nohob: no high order bits
  • nomultiblank: remove all multiple blank lines from a file
  • normal: generate normally distributed random numbers
  • normreg: normalize results from sequence/value linear regression
  • notex: remove tex and latex constructs
  • nulldate: modules to neutralize the date-time functions
  • number: add line numbers to a file
  • numdate: convert tomdate format to a single number
  • odti: munch od and time plates together for xyplo
  • oligosetc: raw sequence to Oligo's Etc format
  • omp: one minus p
  • ordcut: cut out characters based on their ordinality
  • orf: find ORFs for ribosome binding sites
  • palinf: find palindromes, based on information theory
  • parse: breaks a book into its components
  • parseform: parse an html form
  • patana: pattern analysis
  • patlrn: pattern learning
  • patlst: lister of patlrn output.
  • patser: pattern searcher
  • patval: pattern evaluations of aligned sequences
  • pbreak: breaks a file into pages at a certain trigger phrase
  • pcs: partial chi squared
  • pemowe: peptide molecular weights
  • piechart: create a pie chart
  • pizza: make an electronic pizza
  • pnmnormalize: normalize a pnm file to a given size
  • power: raise powerp value to the input value
  • prgmod: programming modules for the delila system
  • protecthtml: protect html file containing less than and greater than
  • pst: paste afile to bfile and send to output
  • quoteline: add quote marks to the beginning of every line in a file
  • range: determine the range of bases in the inst/book
  • rara: rank-rank reformulation of a data set
  • rav: running average information curve
  • rawbk: make a raw sequence into a book
  • rb: remove blanks from ends of lines in a file
  • rean: list new RBS sites and determine if they are in frame with old sites
  • ref2bib: refer to bibtex converter
  • refer: print the references in the pieces of a book
  • reffea: extract references from GenBank entries as lister features
  • reform: raw sequences reformatted
  • rembla: remove blanks from ends of lines in a file
  • rep: records repeats between sequences in two books
  • repro: make multiple copies of a file
  • rf: calculate Rfrequency
  • ri: Rindividual is calculated for every site in the aligned book
  • riden: ring density graph
  • ridi: Ri distribution prediction
  • rila: reformat the ribl table into latex format
  • ring: z space ring
  • rnclean: clean a .newsrc file
  • rndseq: generate random dna sequences
  • round: round a set of numbers
  • roundfile: rounds off a file by droping incomplete last lines
  • rsconv: Compute the convolution between two rsdata files.
  • rseq: rsequence calculated from encoded sequences
  • rsgra: rsequence graph
  • rsim: Rsequence simulation
  • rsub: Subtract Ri for individual bases in a ribl.
  • rv: reverse lines of a file
  • rwbk: make a raw sequence into a book
  • same: counts the number of lines that are identical in two files
  • scan: scan a book with an Ribl weight matrix and generate a vector
  • search: search a book for strings
  • sebo: search for aligned book sequences in another book
  • sepa: separates delila instruction sets
  • setdate: set the date
  • shell: Example Delila System program (an empty shell)
  • short: find locations of short lines in a file
  • shortline: make short lines out of long lines
  • show: show modules in a module library
  • shrink: reduce size of postscript graphics
  • sites: analyse sites from randomized sequence data base
  • siva: site information variance
  • smoothis: smooth a histogram
  • sortbibtex: sort a bibtex database
  • sorth: sort helix list
  • spec: analyse two spectra from the camspec
  • sphere: plot density of shannon spheres
  • split: split a wide file into printable pages
  • spray: spray a genome with random locations
  • sqz: squeeze the input file to fit into fewer characters per line
  • ssbread: read a sample sheet from the ABI sequencer
  • stirling: test of Stirling's formula
  • subfeatures: extract a subset of features from exonfeatures
  • subsymvec: extract a subset of a symvec file
  • sumfile: sum of file sizes
  • surprisal: make the surprisal curve for a histogram
  • swt: switch test for I information computation
  • tabify: convert space delimited table to tab delmiters
  • test: a test program
  • thethepc: find duplicate words in a file
  • timegpc: test time on the GPC compiler
  • timenul: modules to neutralize the date-time functions
  • timep2c: test time on the p2c translator/compiler
  • timesun: test time on the Sun compiler
  • titer: analyse titertek optical density data
  • tkod: read od values from tk data
  • tobinary: convert numbers to binary
  • tod: to database format for sites program
  • todawg: change a book into dawg format
  • tram: transfac matrix analysis
  • transpose: transpose a matrix of integers
  • trex: transfac extraction
  • truncround: plot trunc and round functions
  • tstrnd: test random generator
  • ttest: Student's t-test
  • twogau: 2 dimensional Rayleigh function
  • uncsv: convert csv to plain space table
  • undel: remove references to delman in modules
  • unnumber: remove numbers from a PDF
  • unsqz: unsqueeze the input file
  • untex: remove tex and latex constructs
  • untitle: remove titles from bbl file
  • unverb: remove verbatim sections from a latex file
  • ver: look at the version of a program
  • verbop: increment the version number of a program
  • vernam: print the name of a program associated with the version.
  • vernum: print the version number of a program
  • versave: save the file under the version number
  • vr: Determine the version number and file name of a file.
  • waveplot: normalize sequence locations to B-form DNA coordinates
  • whatch: what characters are in a file?
  • whole: create whole lines
  • winfo: window information curve
  • winrs: Compute Rs/window vs window in a single program
  • winscan: window scan
  • wl: wrap lines in a file
  • woco: word counting program
  • worcha: word changing program
  • worcharev: wordchange reverse
  • wordlist: lists words in a file
  • wtch: what characters are in a file? (unix version)
  • ww: word wrap
  • wwfmt: word wrap like fmt
  • wwlow: word wrap, low order ASCII
  • xyda: back convert histogram to data file
  • xyplo: x, y data plotter (pronounced: "zyplo")
  • yes: supply infinite acknowledgment
  • zipf: Monte Carlo simulation for Peter Shenkin's problem

    Wed Nov 21 00:30:55 EST 2012
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