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
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 of pieces in a book with translation
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
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
mcopy: copy the input to the output only following the first control m
medlinebib: convert medline Unix query format to bibtex format
merge: compare two files and merge them
mergemarks: merge lister marks 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: remove high order bit characters from a file
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
pcdate: test date and time
pcs: partial chi squared
pemowe: peptide molecular weights
pizza: make an electronic pizza
pnmnormalize: normalize a pnm file to a given size
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)
shift: copy one file to another file, with a blank in front of each line
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
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
tipper: copy a file to the output file with special symbols at end
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
tstrnd: test random generator
ttest: Student's t-test
undel: remove references to delman in modules
unnumber: remove numbers from a PDF
unshi: remove first column of characters from a file
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
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.
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
woef: word efficiency
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")
y2k: test whether Pascal compiler gives 2 or 4 digit dates
yes: supply infinite acknowledgment
zipf: Monte Carlo simulation for Peter Shenkin's problem
Thu Nov 29 14:49:41 EST 2007