📄 tfm.usage
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dbifasta Database indexing for fasta file databasesdbiflat Index a flat file databasedbigcg Index a GCG formatted databasedbxfasta Database b+tree indexing for fasta file databasesdbxflat Database b+tree indexing for flat file databasesdbxgcg Database b+tree indexing for GCG formatted databasesdegapseq Removes gap characters from sequencesdescseq Alter the name or description of a sequencediffseq Find differences between nearly identical sequencesdigest Protein proteolytic enzyme or reagent cleavage digestdistmat Creates a distance matrix from multiple alignmentsdomainalign Generate alignments (DAF file) for nodes in a DCF filedomainer Generates domain CCF files from protein CCF filesdomainnr Removes redundant domains from a DCF filedomainrep Reorder DCF file to identify representative structuresdomainreso Remove low resolution domains from a DCF filedomainseqs Adds sequence records to a DCF filedomainsse Add secondary structure records to a DCF filedotmatcher Displays a thresholded dotplot of two sequencesdotpath Non-overlapping wordmatch dotplot of two sequencesdottup Displays a wordmatch dotplot of two sequencesdreg Regular expression search of a nucleotide sequenceeclique Largest clique programeconsense Majority-rule and strict consensus treeecontml Continuous character Maximum Likelihood methodecontrast Continuous character Contrastsedialign Local multiple alignment of sequencesednacomp DNA compatibility algorithmednadist Nucleic acid sequence Distance Matrix programednainvar Nucleic acid sequence Invariants methodednaml Phylogenies from nucleic acid Maximum Likelihoodednamlk Phylogenies from nucleic acid Maximum Likelihood with clockednapars DNA parsimony algorithmednapenny Penny algorithm for DNAedollop Dollo and polymorphism parsimony algorithmedolpenny Penny algorithm Dollo or polymorphismefactor Multistate to binary recoding programefitch Fitch-Margoliash and Least-Squares Distance Methodsegendist Genetic Distance Matrix programehmmalign Align sequences to an HMM profileehmmbuild Build a profile HMM from an alignmentehmmcalibrate Calibrate HMM search statisticsehmmconvert Convert between profile HMM file formatsehmmemit Generate sequences from a profile HMMehmmfetch Retrieve an HMM from an HMM databaseehmmindex Create a binary SSI index for an HMM databaseehmmpfam Search one or more sequences against an HMM databaseehmmsearch Search a sequence database with a profile HMMeinverted Finds DNA inverted repeatsekitsch Fitch-Margoliash method with contemporary tipsemast Motif detectionembossdata Finds or fetches data files read by EMBOSS programsembossversion Writes the current EMBOSS version numberememe Motif detectionemix Mixed parsimony algorithmemma Multiple alignment program - interface to ClustalW programemnu Simple menu of EMBOSS applicationsemowse Protein identification by mass spectrometryeneighbor Phylogenies from distance matrix by N-J or UPGMA methodentret Reads and writes (returns) flatfile entriesepenny Penny algorithm, branch-and-boundepestfind Finds PEST motifs as potential proteolytic cleavage siteseprimer3 Picks PCR primers and hybridization oligoseprotdist Protein distance algorithmeprotpars Protein parsimony algorithmequicktandem Finds tandem repeatserestml Restriction site Maximum Likelihood methodeseqboot Bootstrapped sequences algorithmesim4 Align an mRNA to a genomic DNA sequenceest2genome Align EST and genomic DNA sequencesetandem Looks for tandem repeats in a nucleotide sequenceextractalign Extract regions from a sequence alignmentextractfeat Extract features from a sequenceextractseq Extract regions from a sequencefclique Largest clique programfconsense Majority-rule and strict consensus treefcontml Gene frequency and continuous character Maximum Likelihoodfcontrast Continuous character Contrastsfdiscboot Bootstrapped discrete sites algorithmfdnacomp DNA compatibility algorithmfdnadist Nucleic acid sequence Distance Matrix programfdnainvar Nucleic acid sequence Invariants methodfdnaml Estimates nucleotide phylogeny by maximum likelihoodfdnamlk Estimates nucleotide phylogeny by maximum likelihoodfdnamove Interactive DNA parsimonyfdnapars DNA parsimony algorithmfdnapenny Penny algorithm for DNAfdollop Dollo and polymorphism parsimony algorithmfdolmove Interactive Dollo or Polymorphism Parsimonyfdolpenny Penny algorithm Dollo or polymorphismfdrawgram Plots a cladogram- or phenogram-like rooted tree diagramfdrawtree Plots an unrooted tree diagramffactor Multistate to binary recoding programffitch Fitch-Margoliash and Least-Squares Distance Methodsffreqboot Bootstrapped genetic frequencies algorithmfgendist Compute genetic distances from gene frequenciesfindkm Find Km and Vmax for an enzyme reactionfkitsch Fitch-Margoliash method with contemporary tipsfmix Mixed parsimony algorithmfmove Interactive mixed method parsimonyfneighbor Phylogenies from distance matrix by N-J or UPGMA methodfpars Discrete character parsimonyfpenny Penny algorithm, branch-and-boundfproml Protein phylogeny by maximum likelihoodfpromlk Protein phylogeny by maximum likelihoodfprotdist Protein distance algorithmfprotpars Protein parsimony algorithmfreak Residue/base frequency table or plotfrestboot Bootstrapped restriction sites algorithmfrestdist Distance matrix from restriction sites or fragmentsfrestml Restriction site maximum Likelihood methodfretree Interactive tree rearrangementfseqboot Bootstrapped sequences algorithmfseqbootall Bootstrapped sequences algorithmftreedist Distances between treesftreedistpair Distances between two sets of treesfuzznuc Nucleic acid pattern searchfuzzpro Protein pattern searchfuzztran Protein pattern search after translationgarnier Predicts protein secondary structuregeecee Calculates fractional GC content of nucleic acid sequencesgetorf Finds and extracts open reading frames (ORFs)helixturnhelix Report nucleic acid binding motifshetparse Converts heterogen group dictionary to EMBL-like formathmoment Hydrophobic moment calculationiep Calculates the isoelectric point of a proteininfoalign Information on a multiple sequence alignmentinfoseq Displays some simple information about sequencesinterface Generate inter-chain CON files from CCF filesisochore Plots isochores in large DNA sequenceslibgen Generate discriminating elements from alignmentslindna Draws linear maps of DNA constructslistor Write a list file of the logical OR of two sets of sequencesmakenucseq Creates random nucleotide sequencesmakeprotseq Creates random protein sequencesmarscan Finds MAR/SAR sites in nucleic sequencesmaskfeat Mask off features of a sequencemaskseq Mask off regions of a sequencematcher Finds the best local alignments between two sequencesmatgen3d Generate a 3D-1D scoring matrix from CCF filesmegamerger Merge two large overlapping nucleic acid sequencesmerger Merge two overlapping sequencesmsbar Mutate sequence beyond all recognitionmse Multiple Sequence Editormwcontam Shows molwts that match across a set of filesmwfilter Filter noisy molwts from mass spec outputmyseq Demonstration of sequence readingmytest Demonstration of sequence readingneedle Needleman-Wunsch global alignmentnewcpgreport Report CpG rich areasnewcpgseek Reports CpG rich regionsnewseq Type in a short new sequencenoreturn Removes carriage return from ASCII filesnotseq Exclude a set of sequences and write out the remaining onesnthseq Writes one sequence from a multiple set of sequencesoalistat Statistics for multiple alignment filesoctanol Displays protein hydropathyoddcomp Find protein sequence regions with a biased compositionohmmalign Align sequences with an HMMohmmbuild Build HMMohmmcalibrate Calibrate a hidden Markov modelohmmconvert Convert between HMM formatsohmmemit Extract HMM sequencesohmmfetch Extract HMM from a databaseohmmindex Index an HMM databaseohmmpfam Align single sequence with an HMMohmmsearch Search sequence database with an HMMomeme Motif detectionpalindrome Looks for inverted repeats in a nucleotide sequencepasteseq Insert one sequence into anotherpatmatdb Search a protein sequence with a motifpatmatmotifs Search a PROSITE motif database with a protein sequencepdbparse Parses PDB files and writes protein CCF filespdbplus Add accessibility & secondary structure to a CCF filepdbtosp Convert swissprot:PDB codes file to EMBL-like formatpepcoil Predicts coiled coil regionspepinfo Plots simple amino acid properties in parallelpepnet Displays proteins as a helical netpepstats Protein statisticspepwheel Shows protein sequences as helicespepwindow Displays protein hydropathypepwindowall Displays protein hydropathy of a set of sequencesplotcon Plot quality of conservation of a sequence alignmentplotorf Plot potential open reading framespolydot Displays all-against-all dotplots of a set of sequencespreg Regular expression search of a protein sequenceprettyplot Displays aligned sequences, with colouring and boxingprettyseq Output sequence with translated rangesprimersearch Searches DNA sequences for matches with primer pairsprintsextract Extract data from PRINTSprofit Scan a sequence or database with a matrix or profileprophecy Creates matrices/profiles from multiple alignmentsprophet Gapped alignment for profilesprosextract Build the PROSITE motif database for use by patmatmotifspscan Scans proteins using PRINTSpsiphi Phi and psi torsion angles from protein coordinatesrebaseextract Extract data from REBASErecoder Remove restriction sites but maintain same translationredata Search REBASE for enzyme name, references, suppliers etcremap Display sequence with restriction sites, translation etcrestover Find restriction enzymes producing specific overhangrestrict Finds restriction enzyme cleavage sitesrevseq Reverse and complement a sequencerocon Generates a hits file from comparing two DHF filesrocplot Performs ROC analysis on hits filesscopparse Generate DCF file from raw SCOP filesseealso Finds programs sharing group namesseqalign Extend alignments (DAF file) with sequences (DHF file)seqfraggle Removes fragment sequences from DHF filesseqmatchall All-against-all comparison of a set of sequencesseqnr Removes redundancy from DHF filesseqret Reads and writes (returns) sequencesseqretsplit Reads and writes (returns) sequences in individual filesseqsearch Generate PSI-BLAST hits (DHF file) from a DAF fileseqsort Remove ambiguous classified sequences from DHF filesseqwords Generates DHF files from keyword search of UniProtshowalign Displays a multiple sequence alignmentshowdb Displays information on the currently available databasesshowfeat Show features of a sequenceshoworf Pretty output of DNA translationsshowseq Display a sequence with features, translation etcshuffleseq Shuffles a set of sequences maintaining compositionsigcleave Reports protein signal cleavage sitessiggen Generates a sparse protein signature from an alignmentsiggenlig Generate ligand-binding signatures from a CON filesigscan Generate hits (DHF file) from a signature searchsigscanlig Search ligand-signature library & write hits (LHF file)silent Silent mutation restriction enzyme scansirna Finds siRNA duplexes in mRNAsites Generate residue-ligand CON files from CCF filessixpack Display a DNA sequence with 6-frame translation and ORFsskipseq Reads and writes (returns) sequences, skipping first fewsplitter Split a sequence into (overlapping) smaller sequencesssematch Search a DCF file for secondary structure matchesstretcher Finds the best global alignment between two sequencesstssearch Search a DNA database for matches with a set of STS primerssupermatcher Match large sequences against one or more other sequencessyco Synonymous codon usage Gribskov statistic plottcode Fickett TESTCODE statistic to identify protein-coding DNAtextsearch Search sequence documentation. Slow, use SRS and Entrez!tfextract Extract data from TRANSFACtfm Displays a program's help documentation manualtfscan Scans DNA sequences for transcription factorstmap Displays membrane spanning regionstopo Draws an image of a transmembrane proteintranalign Align nucleic coding regions given the aligned proteinstranseq Translate nucleic acid sequencestrimest Trim poly-A tails off EST sequencestrimseq Trim ambiguous bits off the ends of sequencestwofeat Finds neighbouring pairs of features in sequencesunion Reads sequence fragments and builds one sequencevectorstrip Strips out DNA between a pair of vector sequencesvrnaalifold RNA alignment foldingvrnaalifoldpf RNA alignment folding with partitionvrnacofold RNA cofoldingvrnacofoldconc RNA cofolding with concentrationsvrnacofoldpf RNA cofolding with partitioningvrnadistance RNA distancesvrnaduplex RNA duplex calculationvrnaeval RNA evalvrnaevalpair RNA eval with cofoldvrnafold Calculate secondary structures of RNAsvrnafoldpf Secondary structures of RNAs with partitionvrnaheat RNA meltingvrnainverse RNA sequences matching a structurevrnalfold Calculate locally stable secondary structures of RNAsvrnaplot Plot vrnafold outputvrnasubopt Calculate RNA suboptimalswater Smith-Waterman local alignmentwhichdb Search all databases for an entrywobble Wobble base plotwordcount Counts words of a specified size in a DNA sequencewordfinder Match large sequences against one or more other sequenceswordmatch Finds all exact matches of a given size between 2 sequenceswossname Finds programs by keywords in their one-line documentationyank Reads a sequence range, appends the full USA to a list file Example 4 Display only the groups that the programs can belong to:⌨️ 快捷键说明
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