Command Line Programs

Phylip (Phylogenetic Inference Package) is a software package comprising about 30 command-line programs that cover almost any aspect of phylogenetic analysis... 

For routine database maintenance such as backup, each RDBMS provider typically supplies other command line programs. For example, PostgreSQL provides the pg dump program that outputs a file of SQL commands containing the definition and data contained in each table, schema, etc., in the database. This file becomes a backup of the database, which can be restored using the psql command to execute the SQL commands in the file. 

ZIMPL It was developed in academia by Koch [17], and it is a command line program with a modeling language to translate mathematical programming models to input files for LP and MIP solvers. 

A more recent program from the Johnson lab called CDsstr (current version from July, 2000) may be downloaded via a link from http //www.orst.edu/dept/biochem/johnsondownload.html. This is a 32 bit MS Windows software (command line program). See the file README.CD at the ftp site for more information on the software. 

One significant characteristic of the program is the Command Line. Hereby, the visualization of the molecules is directed in the viewer with commands from a script language. The scripts, such as loop or batch files, can be saved, lutp //openrasmoi.org... 

Alternatively, the user can construct ASCII input files manually. The file format includes many numerical flags to control the type of calculation. The researcher should plan on investing some time in learning to use the program in this way. Jaguar can be executed from the command line, making it possible to use batch processing or job queue systems. 

File Transfer Protocol. A protocol used to move files over the Internet. Typically, you use a command line command, browser capability, or program on your computer called an FTP client to connect to an FTP server found on the Internet. Once connected to the FTP server, you can move files back and forth between your computer and the FTP server. SFTP, Secure FTP, is a more secure protocol for moving data over the Internet in which both your login information and data are encrypted during communications. 

The computer program used in this chapter has been made publicly available under an Open Source Initiative BSD License at http //glare.sourceforge.net. This program is written in C++ and has been successfully compiled on diverse platforms such as Mac OS 10.X, Linux, IBM AIX, and Windows XR Under its current form, GLARE is mainly a command line application that is invoked identically on any of the platforms. Details of the parameters and options can be found at the aforementioned web site. 

If a few simple structure predictions is all you want to do, if you are baffled by the command line, and compiling programs just seems too technical, then web services are for you. 

Several useful sites for doing RNA structure analysis are available on the web. Most of the tasks described below can be performed with the Vienna RNA web server [3] at http / / rna. tbi. uni vie. ac. at /. Currently, it offers web access to the RNAfold, RNAalif old, and RNAinverse programs whose command line usage is shown below. 

Web servers are not ideal for analyzing many or very long sequences. Command line tools, on the other hand, are ideally suited for automating repetitive tasks. They can even be combined in pipes to process the results of one program with another. 

This appendix contains notes on how to start a database for the DB system and instructions on how to run some of the programs described in Chapter 6. When typing lines of commands for programs each line must be completed by a carriage return and in the descriptions below this is often referred to by cr. 

The hierarchical code organization is illustrated in Fig. 18.3. This is by code series and then individual codes. ADAS provides extensive Fortran and IDL subroutine libraries which are available for use in a user s own codes and analysis programs. The IDL subroutines support the user s interface to interactive ADAS and graphical presentation of results. Modular basic atomic calculation routines, utilities and access routines to the ADAS data classes are mostly provided in Fortran but generally with IDL versions which use the Fortran through C wrappers. In particular reaEadf .pro and run-adas.pro IDL procedures give access to ADAS data or run ADAS codes at the IDL command line - independent of interactive ADAS. The libraries now include 700 subroutines. 

As of this writing, DOS 6.22 is the most current MS-DOS version available as a stand-alone operating system. Microsoft has included certain DOS-style command line utilities for use within Windows 95, Windows NT and Windows 2000, but these are actually Windows programs that simply mimic the familiar, old command-prompt environment of DOS. 

Any real understanding of the success of DOS after 1987 requires knowledge of Windows. In the early years of its existence, Microsoft s DOS gained great acceptance and became a standard as a PC operating system. Even so, as computers became more powerful and programs more complex, the limitations of the DOS command-line interface were becoming apparent (as well as the aforementioned conventional memory limitation). 

We will look at a number of graphical utilities in the next few chapters and, believe it or not, the command prompt is one of them. Although you can t tell from looking at it (see Figure 12.20), the crazy thing about the Windows command prompt is that it is actually a 32-bit Windows program that is intentionally designed to have the look and feel of a DOS command line ... 

There are a few options that you can use with the Setup program. To use them, you place them after the SETUP at the command line, separated by a single space. Table 13.2 details these Setup startup switches. 

The MS-DOS backup program MSBACKUP is a very simple, very powerful program. It can be run in either command line mode or with a menu-driven... 

Control Program for Microcomputer (CP/M) A computer operating system that was an early competitor of Microsoft s DOS system. CP/M was a command-line system that was developed by Gary Kildall. 

MS-DOS Acronym for Microsoft Disk Operating System. MS-DOS, like other operating systems, allocates system resources (such as hard and floppy disks, the monitor, and the printer) to the applications programs that need them. MS-DOS is a single-user, single-tasking operating system, with either a command-line interface or a shell interface. 

Once the lattice is created, the bonds are randomly destroyed in a proportion specified at the command line. There is a linked list of sheets in the structure, and each sheet involves a linked list of bonds thus, all bonds are processed using a double nested loop. For each bond, a random number between 0 and 1 is generated and compared to the specified probability (which is also between 0 and 1) if the random number is smaller, the bond is deleted. When a bond is deleted, it acquires the property deleted , which is used later in the program. 

---