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- ...ke GDA, Paup*, Mesquite, ModelTest, '''[[MrBayes]]''', and MacClade. Nexus file names often have a <tt>.nxs</tt> or <tt>.nex</tt> extension. ...ate transitions that take place on branches of a tree, therefore the NEXUS file provides a means to represent a tree (in the standard Newick (a.k.a. New Ha22 KB (1,710 words) - 04:55, 13 September 2006
- The '''dot-star file format''' (or "'''.* format'''") is a standard used in [[phylogenetics]] to == Example dot-star file ==8 KB (764 words) - 04:57, 13 September 2006
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21 bytes (2 words) - 02:02, 26 April 2007
- ...'''portable graymap file format''' ('''PGM''') and the '''portable bitmap file format''' ('''PBM''') specify rules for exchanging graphics files. They pro ...essive conversion programs to turn this code into a [[Windows bitmap|bmp]] file:5 KB (761 words) - 04:02, 14 April 2008
- A '''tab file''' is file format proposed by Rasmus Wernersson for annotating biological sequences.<r ...st/bioperl/Bio/SeqIO/tab.pm Bio::SeqIO::tab]). It is a nearly raw sequence file input/output stream.11 KB (1,628 words) - 01:05, 13 July 2012
- ...:Category:ccp4|Collaborative Computational Project Number 4]] in 1979. The file format for electron density has become industry standard in [[:Category:Cry736 bytes (102 words) - 04:14, 25 April 2007
- The '''HOW file format''' (or just '''HOW file'''). A HOW file consists of entries containing one sequence each. Each entry has the follow5 KB (518 words) - 03:07, 24 June 2007
- ...e is that many different kinds of information can be contained in the same file. Also converting this format into anything else should be simple. *[[Tab file format]]461 bytes (68 words) - 03:05, 24 June 2007
- #REDIRECT [[TAB file format]]29 bytes (4 words) - 07:16, 29 June 2007
Page text matches
- * Remote login, file transfer, etc.: [[Secure Shell|SSH]] (+scp), [[Rsync (command)|rsync]], FTP6 KB (773 words) - 11:35, 5 February 2020
- command &> file ...is simpler to type than the equivalent Bourne shell syntax, "<tt>command > file 2>&1</tt>". Bash, since version 2.05b, can redirect standard input from a34 KB (5,354 words) - 19:04, 9 May 2023
- ; FILENAME: the current file being processed ...file is typically text that is formatted in some way; it can be an actual file, or it can be read by ''Awk'' from the standard input. A typical ''Awk'' pr11 KB (1,785 words) - 21:29, 30 May 2022
- ...]) causing Unix-like operating systems to execute the commands in the text file using a specified interpreter (program) when executed. ...require an interpreter program start with other magic combinations. (See [[File format]] for more details of magic numbers.)5 KB (755 words) - 23:20, 25 May 2006
- // read the data from a text file System.out.println("Can't locate file!");6 KB (738 words) - 17:32, 17 December 2005
- <tr class="data" ><td class="code">:w filename</td> <td>save to new file</td></tr> ...blank character on the line with mark <code>{A-Z0-9}</code> in the correct file:14 KB (2,396 words) - 22:38, 21 June 2023
- ...ctured and stored asking for more powerful tools than the use of files and file systems. On the other hand database systems offer basic mechanisms to struc2 KB (273 words) - 23:35, 25 May 2006
- Elementary Unix with most common commando line file handling and input/output redirection. In the Perl programming language pro1 KB (142 words) - 23:34, 25 May 2006
- The [[NEXUS file format|NEXUS files needed]] in this tutorial are the following: ...where you can enter commands. The next set of commands will load the data file, specify <tt>outgroup</tt>, request that the program should not prompt you28 KB (4,371 words) - 03:28, 14 April 2008
- ...ke GDA, Paup*, Mesquite, ModelTest, '''[[MrBayes]]''', and MacClade. Nexus file names often have a <tt>.nxs</tt> or <tt>.nex</tt> extension. ...ate transitions that take place on branches of a tree, therefore the NEXUS file provides a means to represent a tree (in the standard Newick (a.k.a. New Ha22 KB (1,710 words) - 04:55, 13 September 2006
- == MrBayes tree file scanners == ...ckholm, Sweden (torsten AT bergianska DOT se) makes available MrBayes tree file scanners. These are two [[Perl|Perl scripts]] that scan the output paramete3 KB (373 words) - 02:43, 13 July 2012
- ''note: taken from the <tt>njplot.help</tt> file.'' === >Menu: File ===4 KB (587 words) - 02:42, 13 July 2012
- ...is generated on-the-fly, rather than simply being stored as a static HTML file. The URL is used not only to reference an HTML document at a fixed address, # Index file and Document Root (where the public files are located)11 KB (1,620 words) - 21:43, 15 April 2015
- ...ltiple alignment procedure for proteins and improved support for different file formats. This software was described in Thompson ''et al.'', 1994.<ref name ...onment. For example, in a [[Bash|bash]] console, edit the <tt>.bashrc</tt> file and add the following:16 KB (2,365 words) - 20:40, 6 November 2008
- then in the tree file it is represented by the following sequence of printable characters: The tree starts on the first line of the file, and can continue to subsequent lines. It is best to proceed to a new line,8 KB (1,220 words) - 02:23, 6 March 2009
- \usepackage{epsfig} % place at top of .tex file \psfig{file=output.eps,width=3.25in}13 KB (1,882 words) - 01:17, 24 June 2008
- dev.print(postscript, file="???.ps") #Use this device to save the plot to a file.9 KB (1,378 words) - 22:03, 16 June 2012
- The '''dot-star file format''' (or "'''.* format'''") is a standard used in [[phylogenetics]] to == Example dot-star file ==8 KB (764 words) - 04:57, 13 September 2006
- ** 14.3 Standard File Format5 KB (537 words) - 12:34, 5 January 2006
- <li>Tree file formats</li>20 KB (3,034 words) - 10:55, 6 January 2006
- ...tp://cran.r-project.org/doc/manuals/R-intro.pdf An Introduction to R] (PDF file). library(MASS) # function for writing to file is used6 KB (974 words) - 18:11, 27 March 2012
- ===Encrypt a file=== * Encrypt a file named <code>filename.txt</code> for a single individual (i.e., specify that3 KB (504 words) - 00:08, 25 August 2020
- ...cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -c file:cloudwatchconfig.cfg -s * Amazon Elastic File System28 KB (3,792 words) - 17:56, 26 February 2021
- * File management7 KB (1,028 words) - 20:06, 24 October 2014
- ...org/ PyMedia] — module for wav, mp3, ogg, avi, divx, dvd, cdda, etc. file manipulations.11 KB (1,639 words) - 21:59, 9 September 2022
- $ file $(which mysql_secure_installation) ...n the <tt>/etc</tt> directory). You can also have your own personal config file by creating a <tt>~/.my.cnf</tt> in your home directory.15 KB (2,259 words) - 00:21, 10 February 2021
- In [[:Category:Bioinformatics|bioinformatics]], '''FASTA format''' is a file format used to exchange information between genetic sequence databases. FASTA format files often have file extensions like .fa, .fasta, or .fsa.7 KB (982 words) - 23:02, 13 July 2012
- ...ource for other formats such as the GenBank report. Once a source database file has been formatted by <tt>formatdb</tt> it is not needed by BLAST. Please n -t Title for database file [String]7 KB (1,145 words) - 01:29, 24 July 2008
- ...e to perform a <tt>blastn</tt> search (nucleotide ''vs.'' nucleotide) of a file called <code>QUERY</code> would be: The output is placed into the output file <code>out.QUERY</code> and the search is performed against the "<code>nr</c8 KB (1,298 words) - 00:45, 17 August 2007
- ...t]], and the output is emailed back to the user in three files: one output file, and the two processed proteins. Besides the electrostatic and desolvation15 KB (2,140 words) - 00:25, 24 August 2007
- ...plotting with programs such as [[gnuplot]]. It generates a "SKTTLS Report" file. ...SKTOUT file is given, a copy of this SKTTLS report is also written to that file. Three residuals are calculated for each bond between protein or nucleic ac6 KB (965 words) - 20:57, 2 March 2015
- |'''file''' ''filename'' || display file type of file with name ''filename''1 KB (180 words) - 05:21, 18 May 2007
- ...o longer supported by some browsers. It supports a wide range of molecular file formats.2 KB (306 words) - 01:09, 17 August 2007
- ...between the two files; lines are either shown in the "from file #1", "from file #2", or "in both" columns. This feature can be especially useful when you * The <tt>foo</tt> file has the following lines:1 KB (250 words) - 21:58, 25 May 2006
- ; <tt>filename.inp</tt> : A text file which contains the CHARMM commands. It starts by loading the molecular topo ; <tt>filename.out</tt> : The log file for the CHARMM run, containing echoed commands, and various amounts of comm4 KB (546 words) - 00:49, 3 April 2009
- ...cation (Basic, Digest, NTLM and Negotiate for HTTP and kerberos4 for FTP), file transfer resume, HTTP proxy tunnelling, and many other features. cURL is op The main purpose and use for cURL is to automate unattended file transfers or sequences of operations. It is for example a good tool for sim10 KB (1,538 words) - 04:37, 21 April 2023
- ...ken directly from the agrep [ftp://ftp.cs.arizona.edu/agrep/README README] file.'' ...e> (or in uncompressed form as <code>agrep/agrep-2.04.tar</code>). The tar file contains13 KB (1,944 words) - 06:33, 20 April 2012
- * Download a file and store it locally using a different file name: * Resume large file download:5 KB (719 words) - 07:18, 13 September 2021
- replace from to [from to] ... -- file [file] ... replace from to [from to] ... < file2 KB (371 words) - 05:59, 8 February 2007
- -o|--out fn output file name [stdout]1 KB (196 words) - 01:54, 10 February 2007
- ...rts of the source file which are identical to some part of the destination file, and only sends those parts which cannot be matched in this way. Effectivel *optionally preserves symbolic links, hard links, file ownership, permissions, devices and times13 KB (2,005 words) - 21:34, 11 July 2015
- ...y errors, in which case it will offer to reject the changes or re-edit the file.3 KB (472 words) - 02:01, 26 April 2007
- ...line history then you can still find the commands called in the shell in a file such as <code>.sh_history</code> but if you use a shell such as [[C shell|c1 KB (254 words) - 02:03, 26 April 2007
- ...its the '''[[sudoers]]''' file in a safe fashion. The <code>sudoers</code> file (typically found at <code>/etc/sudoers</code>) allows listed users access t503 bytes (79 words) - 02:04, 26 April 2007
- '''sudoers''' is a [[:Category:Linux Files|file]] (typically located at <code>/etc/sudoers</code>) containing a list of whi The <code>sudoers</code> file is composed of two types of entries: aliases (basically variables) and user2 KB (352 words) - 11:29, 7 July 2014
- ===Running from a file of commands=== ...en a third shell running ghostview to view the eps file. To load a command file:15 KB (2,365 words) - 07:16, 20 April 2012
- ...h one to the whole text file in memory, sed iterates once through the text file applying the whole list of edit commands to each line. Because only one lin ...and then be applied using the ''-f'' option to read the commands from the file:11 KB (1,730 words) - 00:56, 18 May 2015
- ...recursing, change files matching this mask to all upper case, overwrite if file exists:2 KB (329 words) - 00:47, 14 December 2012
- ...[[ISO Images|ISO]] files in Linux. Linux users can easily convert the NRG file using the [[dd]] command in the following way: ==Selecting random lines from a file==20 KB (3,106 words) - 23:38, 10 September 2021
- ...n. That is, it ignores filenames and locations; if the ''contents'' of the file are identical, it will find these files to be identical. It was written by ; <tt>-f --omitfirst</tt> : omit the first file in each set of matches3 KB (442 words) - 01:43, 26 April 2007
- ...at, and the output is e-mailed back to the user in three files: One output file, and the two processed proteins. Besides the electrostatic and desolvation ...to 1500. The email address is where the output/results will be sent (as a file attachment). Hydrogen bonds and missing atoms are built and optimized on th13 KB (1,540 words) - 18:05, 18 February 2012
- ** [[NEXUS file format]]3 KB (524 words) - 00:48, 26 July 2006
- ...rmation specifying the parts that should not be accessed is specified in a file called '''robots.txt''' in the top-level directory of the website.4 KB (662 words) - 23:40, 30 May 2012
- ...ty to customize configuration directives defined in the main configuration file. The configuration directives need to be in <code>.htaccess</code> context :In this case you would need another <code>.htaccess</code> file in <code>/public</code>, containing these lines:7 KB (1,064 words) - 21:41, 15 April 2015
- / </font># identify URLs within a text file<font color="blue">13 KB (2,034 words) - 21:46, 9 March 2009
- == File spacing == * double space a file30 KB (4,929 words) - 22:47, 21 August 2019
- sed [OPTION]... {script-only-if-no-other-script} [input-file]... ...editor is used to perform basic text transformations on an input stream (a file or input from a pipeline). While in some ways similar to an editor which pe8 KB (1,304 words) - 05:58, 7 August 2006
- ; Formatting file contents : <code>fmt pr fold</code> ; Special file types : <code>ln mkdir rmdir mkfifo mknod</code>9 KB (1,324 words) - 23:35, 6 February 2013
- ...longer being used. Processes generally attach to the named pipe (usually a file) to perform inter-process communication. cat file > pipe1 KB (218 words) - 06:54, 19 August 2006
- ...stitution) part creates a FIFO and lets tee listen on it. Then, it uses > (file redirection) to redirect the STDOUT of command to the FIFO that your first ...am reads the output from another with no need for an explicit intermediate file:12 KB (1,905 words) - 20:29, 22 September 2020
- ...ground as daemons. Output that would normally go to the terminal goes to a file called <tt>nohup.out</tt> if it has not already been redirected. ...the command is not run. Any <tt>nohup.out</tt> or <tt>$HOME/nohup.out</tt> file created by <tt>nohup</tt> is made readable and writable only to the user, r3 KB (473 words) - 03:11, 14 April 2008
- <pre>curl ftp://name:passwd@machine.domain:port/full/path/to/file</pre> <pre>curl -u name:passwd ftp://machine.domain:port/full/path/to/file</pre>29 KB (4,993 words) - 01:53, 26 April 2007
- *[[Protein Data Bank (file format)]]1 KB (158 words) - 04:18, 24 April 2007
- ...port] : saves any visible window on an X server and outputs it as an image file. You can capture a single window, the entire screen, or any rectangular por ...ites the original image file, whereas, convert writes to a different image file.3 KB (533 words) - 15:04, 26 February 2011
- == File formats and programs == * The [[Portable pixmap (file format)|portable pixmap/greymap/bitmap formats]] PPM, PGM, PBM. They are co2 KB (245 words) - 06:49, 1 September 2006
- ;jpegtopnm : convert JFIF/JPEG/EXIF file to Netpbm format ;bmptopnm : convert Windows or OS/2 Bitmap file to PPM or PGM17 KB (2,636 words) - 06:49, 1 September 2006
- ...'''portable graymap file format''' ('''PGM''') and the '''portable bitmap file format''' ('''PBM''') specify rules for exchanging graphics files. They pro ...essive conversion programs to turn this code into a [[Windows bitmap|bmp]] file:5 KB (761 words) - 04:02, 14 April 2008
- ...de> file has been removed, this is now set in the <code>/etc/my.cnf</code> file. ...<code>use_mysqld_safe="1"</code> in the <code>/etc/sysconfig/mysqld</code> file to use the old <tt>mysqld_safe</tt> script.7 KB (1,074 words) - 01:52, 3 May 2007
- ...wget]]. The difference is that it is both an accelerator and it splits the file into multiple pieces. --output=f -o f Specify local output file2 KB (258 words) - 01:54, 26 April 2007
- ...'''.netrc''' file contains configuration and autologin information for the File Transfer Protocol client ftp. (''note: It is usually located in your home d The .netrc file contains login and initialization information used by the auto-login proces3 KB (524 words) - 01:04, 5 September 2006
- # Exit the telnet session, and wait for a special end-of-file character. # Exit the ftp session, and wait for a special end-of-file character.7 KB (1,064 words) - 03:05, 13 April 2008
- ...s from C or make complex queries to SGML files based on the [[DTD]] of the file. * Step 1: Create a file called '<code>query</code>' containing the following:3 KB (464 words) - 01:55, 26 April 2007
- ...'''FISH''' requires nothing more than a working shell, and doesn't require file transfer to be enabled on the SSH server. Optionally, there can be a specia ...o be mounted clientside, which reduces hassle when only using FISH for one file.1 KB (170 words) - 05:25, 7 September 2006
- * Step 3: Set directory/file permissions (if not already set): ...r remote server without entering a password. This is useful for automating file transfers. However, it ''must'' be used with care. If not executed properly10 KB (1,480 words) - 18:24, 6 February 2024
- ...e data file that comes with this program, or you can provide your own data file to suit your needs. -f, --file specify units data files (-f '' loads default file)4 KB (615 words) - 22:12, 16 April 2007
- urpmf <file> # Find package that contains a file3 KB (499 words) - 05:50, 17 July 2009
- ;<code>-o</code>:set output file for final image, if written (default test.ppm) ;<code>-O</code>:set output file for mapping data, if written3 KB (581 words) - 06:49, 20 April 2007
- |Essential [[device file|'''dev'''ices]] (e.g., [[:/dev/null]]) |Host-specific system-wide [[configuration file]]s.7 KB (974 words) - 20:12, 19 April 2022
- ...colour <tt>ls</tt> utility <code>/etc/DIR_COLORS</code>. You can copy this file to <code>.dir_colors</code> in your <code>$HOME</code> directory to overrid Below are the colour init strings for the basic file types. A colour init string consists of one or more of the following numeri1 KB (236 words) - 02:08, 9 October 2006
- ...make all the files and other tools involved in generating the final output file (or files). ...nk]] file and would only want the [[fasta]] sequence of the genome. If the file is named "foo.gbk", then one could use gmake to get the fasta sequence: exe6 KB (1,015 words) - 03:38, 1 October 2009
- A '''tab file''' is file format proposed by Rasmus Wernersson for annotating biological sequences.<r ...st/bioperl/Bio/SeqIO/tab.pm Bio::SeqIO::tab]). It is a nearly raw sequence file input/output stream.11 KB (1,628 words) - 01:05, 13 July 2012
- ;<code>-data <file></code> : (required) ;<code>-desctext <file></code> : (optional)5 KB (794 words) - 20:19, 11 July 2012
- #REDIRECT [[Tab file format]]29 bytes (4 words) - 01:14, 17 October 2006
- ;pstops : shuffle pages in a PostScript file (see manpage for details)3 KB (469 words) - 01:21, 8 February 2009
- lines printed. If a file named by an argument cannot be opened for some reason, Perl warns you about it, and moves on to the next file.5 KB (746 words) - 04:15, 31 March 2008
- ...programming language|R]]. It allows you to output your data to an [[SVG]] file. devSVG(file = "Rplots.svg", width = 10, height = 8,715 bytes (95 words) - 01:08, 29 October 2006
- * e.g. add the following to a file in your <tt>/etc/cron.hourly/</tt> dir (after choosing an NTP):783 bytes (126 words) - 02:08, 26 April 2007
- ...n with other programs to provide modular and powerful directory search and file locating capabilities to other commands. * <tt>updatedb</tt> - update a file name database10 KB (1,695 words) - 23:28, 21 May 2015
- ...in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-c ...r more residues, and of which at least 10% are outliers are listed in this file: http://xray.bmc.uu.se/gerard/rama/ramathisweek.txt (Note that this list ma27 KB (3,212 words) - 18:52, 26 July 2012
- To make a HTML file from a wiki file call <tt>wiki.sh</tt> with the wiki file as parameter: This creates a HTML file called <code>MyWiki.html</code>.2 KB (278 words) - 22:31, 2 January 2015
- ; openbabel : A free, open-source version of the Babel chemistry file translation program. (''License: GPL'') ; pine : University of Washington Pine mail user agent. (''License: see file CPYRIGHT'')13 KB (1,598 words) - 06:08, 20 May 2008
- $ tar --index-file=foo.log -jcvf /dev/nst0 /data /home * Or, list files to exclude in a file (one filename per line):6 KB (1,008 words) - 08:58, 17 February 2016
- ...be handled by using the <code>gff</code> option. This specifies a [[GFF]] file that is read from or written to depending on the which way the formatting g ...ript adds a prediction track to LFasta (lfa) entries as specified by a GFF file. This is useful for comparing predictions.7 KB (870 words) - 01:39, 13 July 2012
- This results in a file called <code>cd.iso</code> in folder <code>/tmp</code> which contains all t ...s-NT or Windows-95 machines). The <code>-r</code> is for the directory and file permissions, user/group IDs, etc.11 KB (1,842 words) - 14:44, 14 July 2014
- Create a file called <code>my.dat</code> containing the following (128x128 matrix):453 bytes (60 words) - 00:11, 1 January 2007
- ...that is in the WINDOWS-1252 character set (WinLatin1) and save it as a csv file in the UTF-8 character set. -c : the filename to save the generated csv file as2 KB (364 words) - 05:00, 17 May 2007
- *You can work offline in Firefox just go to File>Work Offline. This means that you can browse your previously visited pages Note: In JRE 1.4.2, this file was in <code>plugin/i386/ns610-gcc32</code>7 KB (1,193 words) - 07:15, 30 April 2010
- ...x Command Line Tools|command-line]] utility to produce a permuted index of file contents similar to a '''[[KWIC]]''' (keywords in their context). It is par -b, --break-file=FILE word break characters in this FILE15 KB (2,341 words) - 02:00, 26 April 2007
- Suppose a file document.txt contains English text lines interspersed with noise lines. To ...and filled with appropriate sample emails. A [[Crontab (command)|crontab]] file can be used to learn the three categories once a day, e.g.7 KB (1,190 words) - 08:53, 22 February 2007
- ''Note: The input file must have four columns: x, y, z (from a PDB structure) and r (radius).''3 KB (480 words) - 04:43, 17 July 2007
