This page describes all the applications provided via the iNquiry software; general help for iNquiry is available here. The majority of these applications are part of the EMBOSS software suite. A mapping between the EMBOSS tools and their GCG equivalent is available from the EMBnet Norway EMBOSS-GCG comparison page. The descriptions of many of the programs below were taken from two excellent sources of documentation: the EMBOSS page and the Pasteur Institute.

Applications here are listed in alphabetical order.

Tool	Description	Source
abiview	Reads ABI file and displays the trace.	EMBOSS
antigenic	Finds antigenic regions of a protein sequence.	EMBOSS
backtranseq	Takes protein seq and estimates the likely nucleic acid sequence by using a codon frequency table.	EMBOSS
banana	Predicts bending of a DNA sequence.	EMBOSS
biosed	Simple sequence editing tool that allows search and replace of a subsequence.	EMBOSS
bl2seq	BLAST one sequence against another to generate a BLAST alignment	Altshul et al.
blast2cours	blast2cours from the NCBI ToolKit	iNquiry
blastall	optimized version of blastall binary from the NCBI ToolKit. Only the blastn algorithm has been optimized for the PowerPC. Otherwise it is the same as the blastall binary from the NCBI Toolkit.	iNquiry
btblastall	wrapper that parallelizes blastall on the cluster.	iNquiry
btwisted	Predicts twisting and stacking energy of a DNA sequence.	EMBOSS
build_icm	Creates and outputs an interpolated Markov Model	S. Salzberg
cai	Calculates the Codon Adaptation Index.	EMBOSS
chaos	Creates a chaos games plot for a sequence.	EMBOSS
charge	Reads a protein sequence and outputs the charges of the amino acids within a window of specified length along the sequence.	EMBOSS
checktrans	Reads a protein sequence with stops and outputs ORFs without stops that meet a minimum size.	EMBOSS
chips	Reads a sequence and calculates the Nc statistic for the effective number of codons used.	EMBOSS
cirdna	Draws a circular DNA map given names and positions of markers.	EMBOSS
clique	Compatibility program for unrooted two-state characters, obtains the largest cliques of characters and the trees that they suggest	J. Felsenstein
clustalw	Generates multi-sequence alignments for DNA or protein sequences.	Des Higgins
codcmp	Reads in two codon usage tables and outputs the differences and usage.	EMBOSS
coderet	Extracts coding regions, mRNA, and protein from feature tables.	EMBOSS
compseq	Counts the composition of subsequences (eg. CG, TTC) in a sequence.	EMBOSS
cons	Generates a consensus sequence from a multiple alignment.	EMBOSS
consense	Reads in a file of trees and generates a consensus tree.	J. Felsenstein
cpgplot	Plots CpG rich regions in a sequence.	EMBOSS
cpgreport	Scans a sequence for CpG rich regions; less specific but more sensitive (will find smaller CpG islands).	EMBOSS
cusp	Reads one or more CDSs and generates a codon usage table.	EMBOSS
cutseq	Sequence editor that allows you to cut a region from the input sequence.	EMBOSS
dan	Calculates DNA/DNA and RNA/DNA melting temperature.	EMBOSS
degapseq	Removes gap/non-alphabetic characters from sequence.	EMBOSS
descseq	Replaces the name/description line of a sequence.	EMBOSS
diffseq	Reports differences between mostly identical sequences (useful when looking for SNPs, etc)	EMBOSS
digest	Finds cleavage positions in a protein.	EMBOSS
distmat	Calculates distance matrix from multiple alignments.	EMBOSS
dnadist	Calculates distance matrix from nucleotide sequences.	J. Felsenstein
dnaml	implements the maximum likelihood method for DNA sequences	J. Felsenstein
dnapars	calculates unrooted parsimony for DNA sequences	J. Felsenstein
dollop	performs Dollo and polymorphism parsimony methods	J. Felsenstein
dotmatcher	Graphs the regions of similarity between two sequences.	EMBOSS
dotpath	Graphs a non-overlapping wordmatch dotplot.	EMBOSS
dottup	Graphs a wordmatch dotplot.	EMBOSS
drawgram	Plots a rooted tree diagram.	J. Felsenstein
drawtree	Plots an unrooted tree diagram.	J. Felsenstein
dreg	Regular expression/pattern match search of DNA sequence.	EMBOSS
einverted	Finds inverted repeats in DNA sequence.	EMBOSS
emma	Interface to ClustalW.	EMBOSS
emowse	Searches protein database for matches with mass spec data.	EMBOSS
entret	Reads a sequence from a database or a file and writes the complete sequence entry to a text file.	Alan Bleasby
eprimer3	Interface to primer3 program; picks primers for PCR and other hybridization oligos.	EMBOSS
equicktandem	Finds tandem repeats in a sequence.	EMBOSS
est2genome	Aligns ESTs and genomic DNA to predict gene calls.	EMBOSS
etandem	Finds tandem repeats in a sequence, identifies repeat sizes and calculates consensus.	EMBOSS
extract	Takes a FASTA format sequence file and a file with a list of start/stop positions in that file and extracts and outputs the specified sequences.	S. Salzberg
extractfeat	Extracts features from a sequence file.	EMBOSS
extractseq	Extracts regions from a sequence (eg. can extract exons to generate a CDS).	EMBOSS
findkm	Determines Km and Vmax based on input of substrate vs. reaction velocity.	EMBOSS
fitch	Performs Fitch-Margoliash, Least Squares, and other methods.	J. Felsenstein
fmtseq	Converts sequence files from one format to another.	Knight
freak	Calculates frequency of bases or residues in a window as it moves along a sequence.	EMBOSS
fuzznuc	Pattern matching for short patterns in nucleic acid sequences.	EMBOSS
fuzzpro	Pattern matching for short patterns in protein sequences.	EMBOSS
fuzztran	Pattern matching for short patterns in translated sequences.	EMBOSS
garnier	Predicts secondary structure of a protein.	Rodrigo Lopez
geecee	Calculates the fraction of GC bases of a sequence.	EMBOSS
getorf	Finds ORFs in a sequence, can define minimum length.	EMBOSS
glimmer	Finds genes in microbial DNA.	Salzburg
graphics	R Graphics demo.	R Development Core Team
helixturnhelix	Finds helix-turn-helix DNA binding motifs in a protein sequence.	EMBOSS
hmmalign	Aligns sequences to an HMM profile.	Eddy
hmmbuild	Builds an HMM profile from a sequence alignment.	Eddy
hmmcalibrate	Reads an HMM file and generates statistics.	Eddy
hmmconvert	Converts files from one HMM file format to another.	Eddy
hmmemit	Reads an HMM file and generates sequences from it.	Eddy
hmmfetch	retrieves an HMM file from an HMM database.	Eddy
hmmpfam	Compares sequences to the HMM profiles in an HMM database.	Eddy
hmmsearch	Reads an HMM file and searches a sequence database for similar sequences.	Eddy
hmoment	Calculates hydrophobic moment of a pepide.	EMBOSS
html4blast	Formats text BLAST results in HTML.	Joly
iep	Calculates the isoelectric point of a protein sequence.	EMBOSS
infoalign	Utility to list properties of sequences in an alignment.	EMBOSS
infoseq	Utility that lists basic information about a sequence (accession number, length, etc)	EMBOSS
isochore	Plots isochores in DNA sequences.	EMBOSS
kitsch	Peforms the Fitch-Margoliash and Least Squares Methods, assumes all tip species are contemporaneous, and an evolutionary clock.	J. Felsenstein
lindna	Draws a linear DNA map given names and positions of markers.	EMBOSS
listor	Reads two sets of sequences and outputs the union of them.	EMBOSS
lmgene	Data transformation and identification of differentially expressed genes in expression arrays.	David M. Rocke
loadseq	Concatenates multiple sequences.	Pasteur
long_orfs	Takes a sequence file (in FASTA format) and outputs a list of all long "potential genes" in it that do not overlap by too much.	S. Salzberg
marscan	Finds matrix/scaffold attachment regions (MAR/SAR sites) in nucleic acid sequences.	EMBOSS
maskfeat	Use to mask off features in a sequence.	EMBOSS
maskseq	Use to mask off regions of a sequence (eg. masking low-complexity regions of a sequence).	EMBOSS
matcher	Compares sequences to find best local alignments between them.	EMBOSS
megamerger	Merges two overlapping DNA sequences, uses less memory than merger, but merger is more accurate for more divergent sequences.	EMBOSS
merger	Merges two overlapping DNA sequences, uses more memory than megamerger, but is more accurate for divergent sequences.	EMBOSS
mix	Applies parsimony with mixed methods.	J. Felsenstein
msbar	Mutates sequences, emulating different forms of mutation.	EMBOSS
mview_blast	Converts results of a BLAST, FASTA, etc. into an alignment of multiple hits against a query; note that it is not in itself an alignment program.	Brown
mwfilter	Filters noise based on molecular wieght from mass spec data.	EMBOSS
needle	Global alignment of two sequences using Needleman-Wunsch algorithm.	EMBOSS
neighbor	Neighbor joining and UPGMA cluster methods.	J. Felsenstein
newcpgreport	Reports CpG rich areas in a sequence.	EMBOSS
newcpgseek	Reports CpG rich areas in a sequence.	EMBOSS
newseq	Creates a new sequence file for short sequences.	EMBOSS
notseq	Excludes a subset of sequences from a file of multiple sequences.	EMBOSS
nthseq	Extracts one sequence from a set of them.	EMBOSS
octanol	Calculates protein hydropathy.	EMBOSS
oddcomp	Finds regions of protein sequences with a biased composition.	EMBOSS
palindrome	Looks for palindromes in nucleic acid sequences.	EMBOSS
pasteseq	Editing tool that allows you to insert a sequence into another at a specified position.	EMBOSS
patmatdb	Takes a protein motif as input and compares it to protein sequence.	EMBOSS
patmatmotifs	Takes a protein sequence as input and searches PROSITE motif database.	EMBOSS
pepcoil	Calculates the probability of a coiled-coil structure in a protein sequence.	EMBOSS
pepinfo	Displays amino acid properties of a protein sequence, can plot hydrophobicity, etc.	EMBOSS
pepnet	Generates helical net for a protein.	EMBOSS
pepstats	Generates calculated protein statistics, for eg. molecular weight, charge, etc.	EMBOSS
pepwheel	Generates helical wheel of protein sequences.	EMBOSS
pepwindow	Generates Kyte and Doolittle hydropathy plot of protein.	EMBOSS
pepwindowall	Generates superimposed Kyte and Doolittle hydropathy plots of a set of aligned proteins.	EMBOSS
phiblast	Searches proteins combining pattern matching with local alignment around the pattern match.	EMBOSS
plotcon	Generates representation of the quality conservation along a set of aligned sequences.	EMBOSS
plotorf	Plots predicted ORFs in a sequence.	EMBOSS
polydot	Generates all-against-all dotplots of a sequence set.	EMBOSS
preg	Regular expression search of a protein sequence.	EMBOSS
prettyplot	Displays aligned sequences, with coloring and boxing.	EMBOSS
prettyseq	Output sequence with translated ranges.	EMBOSS
primersearch	Searches DNA sequences for matches with primer pairs.	EMBOSS
profit	Scan a sequence or database with a matrix or profile.	EMBOSS
prophecy	Creates matrices/profiles from multiple alignments.	EMBOSS
prophet	Gapped alignment for profiles.	EMBOSS
protdist	Computes distance matrix from protein sequences.	J. Felsenstein
protpars	Parsimony method for protein sequences.	J. Felsenstein
pscan	Locates fingerprints (multiple motif features) in a protein sequence.	EMBOSS
psiblast	Iterative protein similarity search; uses position-specific scoring matrices constructed during the search.	Altshul et al.
readseq	Converts DNA or protein sequence files to a specified format.	Gilbert
recoder	Find and remove restriction sites but maintain the same translation.	EMBOSS
redata	Isoschizomers, references and Suppliers for Restriction Enzymes	EMBOSS
remap	Display a sequence with restriction cut sites, translation etc.	EMBOSS
restover	Finds restriction enzymes that produce a specific overhang.	EMBOSS
restrict	Finds restriction enzyme cleavage sites.	EMBOSS
revseq	Reverse and complement a sequence.	EMBOSS
seqmatchall	Does an all-against-all comparison of a set of sequences.	EMBOSS
showdb	Displays information about the currently available local sequence databases.	EMBOSS
showfeat	Show features of a sequence.	EMBOSS
showorf	Pretty output of DNA translations.	EMBOSS
showseq	Display a sequence with features, translation etc.	EMBOSS
shuffleseq	Shuffles a set of sequences maintaining composition	EMBOSS
sigcleave	Predicts signal peptide cleavage sites	EMBOSS
sigscan	Uses protein signature file generated by siggen to find other proteins with that signature	EMBOSS
silent	Silent mutation restriction enzyme scan	EMBOSS
splitter	Split a sequence into (overlapping) smaller sequences.	EMBOSS
stretcher	Global alignment of two sequences.	EMBOSS
stssearch	Searches a DNA database for matches with a set of STS primers	EMBOSS
supermatcher	Finds a match of a large sequence against one or more sequences	EMBOSS
syco	Synonymous codon usage Gribskov statistic plot	EMBOSS
tfscan	Scans DNA sequences for transcription factors.	EMBOSS
tmap	Predict transmembrane proteins	EMBOSS
transeq	Translates nucleic acid sequences	EMBOSS
trimest	Trim poly-A tails off EST sequences	EMBOSS
trimseq	Trim ambiguous bits off the ends of sequences	EMBOSS
vectorstrip	Strips out DNA between a pair of vector sequences	EMBOSS
water	Smith-Waterman local alignment.	EMBOSS
whichdb	Search all databases for an entry	EMBOSS
wise2	Compares a protein sequence to genomic DNA, allowing for introns and frameshifts.	Birney
wobble	Wobble base plot	EMBOSS
wordcount	Counts words of a specified size in a DNA sequence.	EMBOSS
wordmatch	Finds all exact matches of a given size between 2 sequences	EMBOSS
xblast	Reads blast results and generates a query with the hits masked.	Claverie