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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
