📄 tfm.txt
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tfm Function Displays a program's help documentation manualDescription This program displays the help documentation for an EMBOSS program. The contributors of the EMBOSS programs do attempt to provide an adequate description of the programs. This documentation for your current release is included as HTML pages in the EMBOSS distribution and may be available at your site. The latest documentation for the next release is provided by the developers at http://emboss.sourceforge.net/apps/ The release documentation is also available however through the program tfm as normal text. If you have problems understanding the function or usage of an EMBOSS program, then you should contact the EMBOSS mailing list (emboss@emboss.open-bio.org). The unusual name of this program comes from the common computing science expression: RTFM. This acronym, as you probably already know, stands for Read The Fine* Manual; so this is The Fine* Manual. * Insert the expletive of your choice here! Paged text output to the screen tfm is unusual for an EMBOSS program in that it expects to be used interactively and so it displays the documentation text a page at a time, pausing after every page for the user to press the SPACE bar on their keyboard. (i.e. it uses the UNIX program more to display the information). This behaviour can be turned off by using the qualifier -nomore. The text is paged to the screen using the UNIX program 'more'. The program 'more' is a very standard way for text files to be displayed in UNIX. You might, however, prefer the text to be displayed using other programs, for example 'less' (which has more functionality than 'more' and is used by many people). The UNIX environment variable 'PAGER' can be set to hold the name of your preferred program. If you have PAGER set, then tfm will use this specified program instead of using the default 'more' program. (If you want tfm to use a specified program that is different to the normal 'PAGER' program, then 'PAGER' can be overriden by setting the environment variable 'EMBOSS_PAGER' to hold the name of the program that should only be used to display text in tfm). 'PAGER' can be set in UNIX by a command like: setenv PAGER less To get help on 'more' when using it to display text, press the '?' key. To get help on 'less' when using it to display text, press the 'h' key.Usage Here is a sample session with tfm% tfm wossname Displays a program's help documentation manual::::::::::::::/homes/pmr/local/share/EMBOSS/doc/programs/text/wossname.txt:::::::::::::: wossnameFunction Finds programs by keywords in their one-line documentationDescription This allows a user to search for keywords or parts of words in the brief documentation (as displayed by a program when it first starts). The program name and the brief description is output. If no words to search for are specified, then details of all the EMBOSS programs are output. The program has been written on the assumption that most people will use it to quickly find the name of a program based on that program's description, so the output goes to the screen by default. This program may find some use in automatically generating lists of EMBOSS programs and their groups for Web pages.Usage Here is a sample session with wossname Search for programs with 'restrict' in their description:% wossname restrictFinds programs by keywords in their one-line documentationSEARCH FOR 'RESTRICT'erestml Restriction site Maximum Likelihood methodfrestboot Bootstrapped restriction sites algorithmfrestdist Distance matrix from restriction sites or fragmentsfrestml Restriction site maximum Likelihood methodrecoder 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 scan Example 2 Display a listing of programs in their groups:% wossname -search ''Finds programs by keywords in their one-line documentationACDacdc ACD compileracdpretty ACD pretty printing utilityacdtable Creates an HTML table from an ACD fileacdtrace ACD compiler on-screen traceacdvalid ACD file validationALIGNMENT CONSENSUScons Creates a consensus from multiple alignmentsmegamerger Merge two large overlapping nucleic acid sequencesmerger Merge two overlapping sequencesALIGNMENT DIFFERENCESdiffseq Find differences between nearly identical sequencesALIGNMENT DOT PLOTSdotmatcher Displays a thresholded dotplot of two sequencesdotpath Non-overlapping wordmatch dotplot of two sequencesdottup Displays a wordmatch dotplot of two sequencespolydot Displays all-against-all dotplots of a set of sequencesALIGNMENT GLOBALesim4 Align an mRNA to a genomic DNA sequenceest2genome Align EST and genomic DNA sequencesneedle Needleman-Wunsch global alignmentstretcher Finds the best global alignment between two sequencesALIGNMENT LOCALmatcher Finds the best local alignments between two sequencesseqmatchall All-against-all comparison of a set of sequencessupermatcher Match large sequences against one or more other sequenceswater Smith-Waterman local alignmentwordfinder Match large sequences against one or more other sequenceswordmatch Finds all exact matches of a given size between 2 sequencesALIGNMENT MULTIPLEedialign Local multiple alignment of sequencesemma Multiple alignment program - interface to ClustalW programinfoalign Information on a multiple sequence alignmentmse Multiple Sequence Editorplotcon Plot quality of conservation of a sequence alignmentprettyplot Displays aligned sequences, with colouring and boxingshowalign Displays a multiple sequence alignmenttranalign Align nucleic coding regions given the aligned proteinsDISPLAYabiview Reads ABI file and display the tracecirdna Draws circular maps of DNA constructslindna Draws linear maps of DNA constructspepnet Displays proteins as a helical netpepwheel Shows protein sequences as helicesprettyplot Displays aligned sequences, with colouring and boxingprettyseq Output sequence with translated rangesremap Display sequence with restriction sites, translation etcseealso Finds programs sharing group namesshowalign Displays a multiple sequence alignmentshowdb Displays information on the currently available databasesshowfeat Show features of a sequenceshowseq Display a sequence with features, translation etcsixpack Display a DNA sequence with 6-frame translation and ORFstextsearch Search sequence documentation. Slow, use SRS and Entrez!EDITbiosed Replace or delete sequence sectionscodcopy Reads and writes a codon usage tablecutseq Removes a specified section from a sequencedegapseq Removes gap characters from sequencesdescseq Alter the name or description of a sequenceentret Reads and writes (returns) flatfile entriesextractalign Extract regions from a sequence alignmentextractfeat Extract features from a sequenceextractseq Extract regions from a sequencelistor Write a list file of the logical OR of two sets of sequencesmakenucseq Creates random nucleotide sequencesmakeprotseq Creates random protein sequencesmaskfeat Mask off features of a sequencemaskseq Mask off regions of a sequencenewseq 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 sequencespasteseq Insert one sequence into anotherrevseq Reverse and complement a sequenceseqret Reads and writes (returns) sequencesseqretsplit Reads and writes (returns) sequences in individual filesskipseq Reads and writes (returns) sequences, skipping first fewsplitter Split a sequence into (overlapping) smaller sequencestrimest Trim poly-A tails off EST sequencestrimseq Trim ambiguous bits off the ends of sequencesunion Reads sequence fragments and builds one sequencevectorstrip Strips out DNA between a pair of vector sequencesyank Reads a sequence range, appends the full USA to a list fileENZYME KINETICSfindkm Find Km and Vmax for an enzyme reactionFEATURE TABLEScoderet Extract CDS, mRNA and translations from feature tablesextractfeat Extract features from a sequencemaskfeat Mask off features of a sequenceshowfeat Show features of a sequencetwofeat Finds neighbouring pairs of features in sequencesHMMehmmalign 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 HMMoalistat Statistics for multiple alignment filesohmmalign 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 HMMINFORMATIONinfoalign Information on a multiple sequence alignmentinfoseq Displays some simple information about sequencesseealso Finds programs sharing group namesshowdb Displays information on the currently available databasestextsearch Search sequence documentation. Slow, use SRS and Entrez!tfm Displays a program's help documentation manualwhichdb Search all databases for an entrywossname Finds programs by keywords in their one-line documentationMENUSemnu Simple menu of EMBOSS applicationsNUCLEIC 2D STRUCTUREeinverted Finds DNA inverted repeatsvrnaalifold 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 CODON USAGEcai CAI codon adaptation indexchips Codon usage statisticscodcmp Codon usage table comparisoncusp Create a codon usage tablesyco Synonymous codon usage Gribskov statistic plotNUCLEIC COMPOSITIONbanana Bending and curvature plot in B-DNAbtwisted Calculates the twisting in a B-DNA sequencechaos Create a chaos game representation plot for a sequencecompseq Count composition of dimer/trimer/etc words in a sequencedan Calculates DNA RNA/DNA melting temperaturefreak Residue/base frequency table or plot⌨️ 快捷键说明
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