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
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 Delila instructions
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
csv2ssv: convert a comma delimited csv file to a space delimited 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
dedup: remove character duplications
dehtml: remove html structures
delila: the librarian for sequence manipulation
delinst: create delila instructions from lists
delmod: delila module library
dem: decimal-match
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
despace: remove space character duplications
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
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
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
evenco: even column - read integers from a file and output with leading spaces
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.
fealoc: feature location in a genome
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
floc: fast find features of highest Ri in a given sequence range
fpcfix: add assign to pascal programs
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
gedo: gene dosage
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
hc: H-curve and H uncertainty
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
multibest: find features with the highest Ri in a given sequence range
multiscan: scan a Delila system book for many multipart 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
nocomequal: 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
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
rebasec: convert restriction enzyme list to dimensionality
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
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
scale: scale a column of a table
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: One line description: 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
timefpc: test time on the Free Pascal (fpc) compiler
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
todobfcite: find cite inside todobf of a LaTeX document
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: plot sites around the wave of B-form DNA
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)
wtco: what characters are in a file? counts
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
Fri Mar 22 00:02:08 EDT 2024