📄 tfm.usage
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palindrome Looks for inverted repeats in a nucleotide sequenceNUCLEIC RESTRICTIONrecoder 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 sitesshowseq Display a sequence with features, translation etcsilent Silent mutation restriction enzyme scanNUCLEIC RNA FOLDINGvrnaalifold 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 suboptimalsNUCLEIC TRANSCRIPTIONtfscan Scans DNA sequences for transcription factorsNUCLEIC TRANSLATIONbacktranambig Back translate a protein sequence to ambiguous codonsbacktranseq Back translate a protein sequencecoderet Extract CDS, mRNA and translations from feature tablesplotorf Plot potential open reading framesprettyseq Output sequence with translated rangesremap Display sequence with restriction sites, translation etcshoworf Pretty output of DNA translationsshowseq Display a sequence with features, translation etcsixpack Display a DNA sequence with 6-frame translation and ORFstranseq Translate nucleic acid sequencesPHYLOGENY CONSENSUSeconsense Majority-rule and strict consensus treefconsense Majority-rule and strict consensus treeftreedist Distances between treesftreedistpair Distances between two sets of treesPHYLOGENY CONTINUOUS CHARACTERSecontml Continuous character Maximum Likelihood methodecontrast Continuous character Contrastsfcontrast Continuous character ContrastsPHYLOGENY DISCRETE CHARACTERSeclique Largest clique programedollop Dollo and polymorphism parsimony algorithmedolpenny Penny algorithm Dollo or polymorphismefactor Multistate to binary recoding programemix Mixed parsimony algorithmepenny Penny algorithm, branch-and-boundfclique Largest clique programfdollop Dollo and polymorphism parsimony algorithmfdolpenny Penny algorithm Dollo or polymorphismffactor Multistate to binary recoding programfmix Mixed parsimony algorithmfmove Interactive mixed method parsimonyfpars Discrete character parsimonyfpenny Penny algorithm, branch-and-boundPHYLOGENY DISTANCE MATRIXefitch Fitch-Margoliash and Least-Squares Distance Methodsekitsch Fitch-Margoliash method with contemporary tipseneighbor Phylogenies from distance matrix by N-J or UPGMA methodffitch Fitch-Margoliash and Least-Squares Distance Methodsfkitsch Fitch-Margoliash method with contemporary tipsfneighbor Phylogenies from distance matrix by N-J or UPGMA methodPHYLOGENY GENE FREQUENCIESegendist Genetic Distance Matrix programfcontml Gene frequency and continuous character Maximum Likelihoodfgendist Compute genetic distances from gene frequenciesPHYLOGENY MOLECULAR SEQUENCEdistmat Creates a distance matrix from multiple alignmentsednacomp 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 DNAeprotdist Protein distance algorithmeprotpars Protein parsimony algorithmerestml Restriction site Maximum Likelihood methodeseqboot Bootstrapped sequences algorithmfdiscboot 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 DNAfdolmove Interactive Dollo or Polymorphism Parsimonyffreqboot Bootstrapped genetic frequencies algorithmfproml Protein phylogeny by maximum likelihoodfpromlk Protein phylogeny by maximum likelihoodfprotdist Protein distance algorithmfprotpars Protein parsimony algorithmfrestboot Bootstrapped restriction sites algorithmfrestdist Distance matrix from restriction sites or fragmentsfrestml Restriction site maximum Likelihood methodfseqboot Bootstrapped sequences algorithmfseqbootall Bootstrapped sequences algorithmPHYLOGENY TREE DRAWINGfdrawgram Plots a cladogram- or phenogram-like rooted tree diagramfdrawtree Plots an unrooted tree diagramfretree Interactive tree rearrangementPROTEIN 2D STRUCTUREgarnier Predicts protein secondary structurehelixturnhelix Report nucleic acid binding motifshmoment Hydrophobic moment calculationpepcoil Predicts coiled coil regionspepnet Displays proteins as a helical netpepwheel Shows protein sequences as helicestmap Displays membrane spanning regionstopo Draws an image of a transmembrane proteinPROTEIN 3D STRUCTUREcontacts Generate intra-chain CON files from CCF filesdomainalign Generate alignments (DAF file) for nodes in a DCF filedomainrep Reorder DCF file to identify representative structuresdomainreso Remove low resolution domains from a DCF fileinterface Generate inter-chain CON files from CCF fileslibgen Generate discriminating elements from alignmentsmatgen3d Generate a 3D-1D scoring matrix from CCF filespsiphi Phi and psi torsion angles from protein coordinatesrocon Generates a hits file from comparing two DHF filesrocplot Performs ROC analysis on hits filesseqalign Extend alignments (DAF file) with sequences (DHF file)seqfraggle Removes fragment sequences from DHF 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 UniProtsiggen 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)PROTEIN COMPOSITIONbacktranambig Back translate a protein sequence to ambiguous codonsbacktranseq Back translate a protein sequencecharge Protein charge plotchecktrans Reports STOP codons and ORF statistics of a proteincompseq Count composition of dimer/trimer/etc words in a sequenceemowse Protein identification by mass spectrometryfreak Residue/base frequency table or plotiep Calculates the isoelectric point of a proteinmwcontam Shows molwts that match across a set of filesmwfilter Filter noisy molwts from mass spec outputoctanol Displays protein hydropathypepinfo Plots simple amino acid properties in parallelpepstats Protein statisticspepwindow Displays protein hydropathypepwindowall Displays protein hydropathy of a set of sequencesPROTEIN MOTIFSantigenic Finds antigenic sites in proteinsdigest Protein proteolytic enzyme or reagent cleavage digestemast Motif detectionememe Motif detectionepestfind Finds PEST motifs as potential proteolytic cleavage sitesfuzzpro Protein pattern searchfuzztran Protein pattern search after translationhelixturnhelix Report nucleic acid binding motifsoddcomp Find protein sequence regions with a biased compositionomeme Motif detectionpatmatdb Search a protein sequence with a motifpatmatmotifs Search a PROSITE motif database with a protein sequencepepcoil Predicts coiled coil regionspreg Regular expression search of a protein sequencepscan Scans proteins using PRINTSsigcleave Reports protein signal cleavage sitesPROTEIN MUTATIONmsbar Mutate sequence beyond all recognitionshuffleseq Shuffles a set of sequences maintaining compositionPROTEIN PROFILESprofit Scan a sequence or database with a matrix or profileprophecy Creates matrices/profiles from multiple alignmentsprophet Gapped alignment for profilesTESTcrystalball Answers every drug discovery question about a sequencemyseq Demonstration of sequence readingmytest Demonstration of sequence readingUTILS DATABASE CREATIONaaindexextract Extract data from AAINDEXallversusall Sequence similarity data from all-versus-all comparisoncathparse Generates DCF file from raw CATH filescutgextract Extract data from CUTGdomainer Generates domain CCF files from protein CCF filesdomainnr Removes redundant domains from a DCF filedomainseqs Adds sequence records to a DCF filedomainsse Add secondary structure records to a DCF filehetparse Converts heterogen group dictionary to EMBL-like formatpdbparse Parses PDB files and writes protein CCF filespdbplus Add accessibility & secondary structure to a CCF filepdbtosp Convert swissprot:PDB codes file to EMBL-like formatprintsextract Extract data from PRINTSprosextract Build the PROSITE motif database for use by patmatmotifsrebaseextract Extract data from REBASEscopparse Generate DCF file from raw SCOP filesseqnr Removes redundancy from DHF filessites Generate residue-ligand CON files from CCF filesssematch Search a DCF file for secondary structure matchestfextract Extract data from TRANSFACUTILS DATABASE INDEXINGdbiblast Index a BLAST databasedbifasta 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 databasesUTILS MISCembossdata Finds or fetches data files read by EMBOSS programsembossversion Writes the current EMBOSS version number Example 3 Display an alphabetic listing of all programs:% wossname -search '' -alphabetic Finds programs by keywords in their one-line documentationALPHABETIC LIST OF PROGRAMSaaindexextract Extract data from AAINDEXabiview Reads ABI file and display the traceacdc ACD compileracdpretty ACD pretty printing utilityacdtable Creates an HTML table from an ACD fileacdtrace ACD compiler on-screen traceacdvalid ACD file validationallversusall Sequence similarity data from all-versus-all comparisonantigenic Finds antigenic sites in proteinsbacktranambig Back translate a protein sequence to ambiguous codonsbacktranseq Back translate a protein sequencebanana Bending and curvature plot in B-DNAbiosed Replace or delete sequence sectionsbtwisted Calculates the twisting in a B-DNA sequencecai CAI codon adaptation indexcathparse Generates DCF file from raw CATH fileschaos Create a chaos game representation plot for a sequencecharge Protein charge plotchecktrans Reports STOP codons and ORF statistics of a proteinchips Codon usage statisticscirdna Draws circular maps of DNA constructscodcmp Codon usage table comparisoncodcopy Reads and writes a codon usage tablecoderet Extract CDS, mRNA and translations from feature tablescompseq Count composition of dimer/trimer/etc words in a sequencecons Creates a consensus from multiple alignmentscontacts Generate intra-chain CON files from CCF filescpgplot Plot CpG rich areascpgreport Reports all CpG rich regionscrystalball Answers every drug discovery question about a sequencecusp Create a codon usage tablecutgextract Extract data from CUTGcutseq Removes a specified section from a sequencedan Calculates DNA RNA/DNA melting temperaturedbiblast Index a BLAST database⌨️ 快捷键说明
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