Free io 0.17 rc6 software for linux

Bio::Phylo::IO Perl module contains input and output of phylogenetic data.

SYNOPSIS

use Bio::Phylo::IO;

# parsing a tree from a newick string
my $tree_string = (((A,B),C),D);;
my $tree = Bio::Phylo::IO->parse(
-string => $tree_string,

# old parser, always adds node labels
-format => newick,
)->first;

# note: newick parsers return
# Bio::Phylo::Forest! Call
# ->first to retrieve the first
# tree of the forest.

# prints Bio::Phylo::Forest::Tree
print ref $tree, "n";

# parsing a table
my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1);
my $matrix = Bio::Phylo::IO->parse(
-string => $table_string,
-format => table,

# Data type, see Bio::Phylo::Parsers::Table
-type => STANDARD,

# field separator
-fieldsep => ,,

# line separator
-linesep => |
);

# prints Bio::Phylo::Matrices::Matrix
print ref $matrix, "n";

# parsing a list of taxa
my $taxa_string = A:B:C:D;
my $taxa = Bio::Phylo::IO->parse(
-string => $taxa_string,
-format => taxlist,
-fieldsep => :
);

# prints Bio::Phylo::Taxa
print ref $taxa, "n";

# matches taxon names in tree to $taxa object
$tree->cross_reference($taxa);

# likewise for matrix
$matrix->cross_reference($taxa);

print Bio::Phylo::IO->unparse(

# pass the tree object,
# crossreferenced to taxa, which
# are crossreferenced to the matrix
-phylo => $tree,
-format => pagel
);

# prints a pagel data file:
#4 2
#A,n1,0.000000,1,2
#B,n1,0.000000,1,2
#n1,n2,0.000000
#C,n2,0.000000,2,2
#n2,n3,0.000000
#D,n3,0.000000,2,1

SLAX is a small bootable CD containing the Linux operating system. SLAX distirbution runs Linux directly from the CD (or USB) without installing.
The Live CD described here is based on the Slackware Linux distribution and is downloadable from this website as an ISO image.
The primary goal of SLAX is to provide a wide collection of useful software while keeping the cds image small enough to be written to a 185 MB CD-R(W) medium (small 8 cm CD). SLAX boots directly from the CD or USB devices and it provides a full featured Linux operating system.
All your available partitions and data storage devices (CD-ROM, USB storage devices, etc.) should be recognized at boot and should be mounted to /mnt/xx. As an example, "disc0part1" may be assigned to the first partition on your primary hard drive, "disc1part1" for your USB storage device, or "cdrom0" for your CD-ROM drive. SLAX will never write anything to the mounted devices. Mounting is safe and does not change the data.
After booting, you should be able to login as a "root", with the password "toor"; both without quotes, of course.
When logged in, you have many options. At the shell prompt, you may start Midnight Commander (type "mc" to the console), play some music from your hard drive (type "play /mnt/path/file.mp3"), adjust your audio volume (type "alsamixer"), configure IP address (type "netconfig") or browse web pages with the text-based browser (type "lynx http://url").
To start the graphical environment included with SLAX, type "gui" (for graphical user interface). It will attempt to autoconfigure your graphics card, monitor, keyboard and mice, and if successful it will run an X session with KDE. Im pretty sure that you will know how to get around at this point. :-) Use "guisafe" instead of "gui" for safe-mode (VESA framebuffer) without autodetection.
In the unfortunate case your mouse doesnt work, try to move it for a few seconds to see if it will be autodetected. If it isnt, shut down Xwindow (press Ctrl+Alt+Backspace) and start it again. If this wont help then you are using something I have not included in the autoconfiguration process (COM2 mouse?). If you are comfortable with bash, or you atleast understand how to make your favorite mouse function under Linux, try to modify the symbolic link /dev/mouse manually.
If you dont like the autoconfigured screen resolution, refresh rate, or the K Desktop Environment, start "gui" with some additional options. Try for example "gui 800x600 60", where 800x600 is the desired screen resolution and 60 is the desired refresh rate. Fluxbox is one of the other window managers included and may be called with "guifast" or "gui fluxbox". In any event, type "gui --help" for more information.
All scripts and source code are available and can be used to build your own Live CD.
SLAX is available as an ISO image of the CD. It fits on small 8cm CD-R(W). Burn it with your favorite cd-writing software and then boot from the CD.
You might want to check your BIOS to assure its set to boot the CD prior the disc.
SLAX CD contains:
- Linux Kernel 2.4.28-pre4 with SATA support
- X.org 6.8.1
- KDE 3.3.1
- KOffice 1.3.3
- KDE games
- MPlayer 1.0pre5 with KPlayer
- kopete ICQ/AIM/Y!/IRC
- midnight commander
- rdesktop (rscp in KDE)
- hotplug support
- cdrtools
- k3b burning GUI for KDE
- mutt email client
- wget
- and much more...

TAC project is a pure Tcl version of AOL Instant Messenger (AIM).
The TAC client began its life as a small add-on program distributed with TiK, the Tcl/Tk client.
TAC has only a few of the features found in native Windows and Macintosh clients.
It is easy for users to add features to TAC using Tcl. TAC is meant to give users with only console access the ability to use AOL Instant Messenger.
Enhancements:
- Small bug fixed with away package that allows numbers in away messages
- Mobile phone package added
- New Away command: /awayfile or a:f sets the away message to the contents of the filename supplied as an argument
- Bugs fixed with shell escape function

iLaunch is designed to clear up clutter on your desktop by stacking icons in a scrollable format. (think deck of cards) Using the scroll wheel on your mouse (button 4 & 5) will cycle through the applications in the .rc file added by you the user from the first application to the end.
Then it will loop to the beginning, being an endless loop cycling through your stack of icons.
Main features:
- Background image or no background image support(transparent background).
- Maximizes desktop space by moving all your icons into one scrollable stack.
- Drag and Drop support when dragging from the K-menu or the Kicker bar(no Desktop icons or devices yet).
- No wheel mouse support, by right clicking the theme and selecting the No Wheel Mouse option in the Configure theme menu.
- Alternate display text when adding applications to customize what is displayed to your needs.
- Icon theme finding engine to locate your current icons being used by KDE.
- Mouse over highlighting when on an application to launch.
- Custom icons support by selecting the directory in which they are stored.
- Drag and drop a file onto iLaunch and the application displayed will launch it for you if the type is correct.
- Applications that support multiple files being opened via command line should be able to accept multi-file drops as well.
- Ability to select a unique icon for the showing application and it is remembered when changing icon themes as well.
- Automatic resizing to suit the icon theme selected when setting the Custom Icon Directory
- Remove the current application by right clicking and selecting it from the Configure menu.
- Middle clicking iLaunch displays the information about the execution command and the location of the icon its using.

Slirp provides a SLIP/PPP emulator over shell/telnet/ssh/etc.
Slirp is a (C)SLIP/PPP emulator based on the original BSD sources. It allows the user to pull up a full internet connection over a shell connection, and features sharing multiple modems for additional bandwidth.
Slirp emulates a PPP or SLIP connection over a normal terminal. This is an actual PPP or SLIP link, firewalled for peoples protection.
It makes a quick way to connect your Palm Pilot over the Internet via your Unix or Linux box!!! You dont need to mess around with your /etc/inetd.conf or your /etc/ppp/options on your system.
Slirp works on most Unix platforms, including:
Linux glibc and libc5 systems
Solaris 2.x
OSF/1
or any Unix that can compile GNU autoconfed programs with GCC.
Palm Pilot users can use this to connect their PalmOS device to the system and onto the Internet, using their home computer as a host. If you need to raise a temporary link, or cant run pppd, Slirp may help.
Enhancements:
- Changes for operation under Cygwin
- Added patch for Cygwin I_PUSH by Michael Wetherell
- dns is now transferred to peer, (If compiled with -DUSE_MS_DNS) (Ripped off from hacked pppd version 2.2.0f)
- Two dns options can be specified on command line, (Only the first is used internally, but both will get transferred to peer)
- Has a hack for connecting to a MS direct cable connect (If compiled with -DMS_DCC) Only works when PPP (-P option) is chosen, but gives effectively a nated direct cable connect. (A chat script option would be nicer)
- Fix to exit code that incorrectly iterated list of ttys attached
- Fixes to terminal restore code, No longer closes stdin on exit
- If stdout, or stderr are redirected, it wont close them (so you can debug using fprintf(stderr...)
- No longer removes 0s, 1s from incoming data stream
- New Option nozeros to not look at strings of 0s, 1s to cause exit/suspend (See docs/CONFIG)
- Can specify alternate tty on command line using "tty ttydevice" (Overrides SLIRP_TTY environment variable) (see docs/CONFIG)
- Debug builds log raw incoming data, and ppp checksum fault packets
- Minor documentation updates
- Does not close all file handles, (Pain when trying to debug)
- Can manually turn on early debugging in main()
- Most of Tims security fixes in place, (It is still insecure...) Probably snprintf will make slirp less portable.

OpenL2TP is an open source L2TP client / server, written by Katalix Systems specifically for Linux. The project has been designed for use as an enterprise L2TP VPN server or in commercial, Linux-based, embedded networking products and is able to support hundreds of sessions, each with different configuration.
A userspace daemon handles the L2TP control protocol and a kernel component handles the datapath. The distribution includes kernel patches for 2.4 and 2.6, a pppd plugin, a command line application for management and documentation. Other PPP implementations may be used instead of pppd by use of an OpenL2TP plugin.
Enhancements:
- This release adds a mechanism by which individual L2TP sessions will automatically retry if the peer drops the connection.
- This feature is useful for ISPs that use multiple sessions in a single L2TP tunnel.
- Support for the Linux 2.6.20 kernel has been added.
- New pre-built RPMs for FC5/FC6 kernel updates are also available.

GNU Octave project is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octaves own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.

GNU Octave is also freely redistributable software. You may redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation.

Octave was written by John W. Eaton and many others. Because Octave is free software you are encouraged to help make Octave more useful by writing and contributing additional functions for it, and by reporting any problems you may have.

Command line options:

Here is a complete list of all the command line options that Octave accepts.

--debug
-d
Enter parser debugging mode. Using this option will cause Octaves parser to print a lot of information about the commands it reads, and is probably only useful if you are actually trying to debug the parser.

--echo-commands
-x
Echo commands as they are executed.

--exec-path path
Specify the path to search for programs to run. The value of path specified on the command line will override any value of OCTAVE_EXEC_PATH found in the environment, but not any commands in the system or user startup files that set the built-in variable EXEC_PATH.

--help
-h
-?
Print short help message and exit.

--info-file filename
Specify the name of the info file to use. The value of filename specified on the command line will override any value of OCTAVE_INFO_FILE found in the environment, but not any commands in the system or user startup files that set the built-in variable INFO_FILE.

--info-program program
Specify the name of the info program to use. The value of program specified on the command line will override any value of OCTAVE_INFO_PROGRAM found in the environment, but not any commands in the system or user startup files that set the built-in variable INFO_PROGRAM.

--interactive
-i
Force interactive behavior. This can be useful for running Octave via a remote shell command or inside an Emacs shell buffer. For another way to run Octave within Emacs, see D. Emacs Octave Support.

--no-history
-H
Disable command-line history.

--no-init-file
Dont read the `~/.octaverc or `.octaverc files.

--no-line-editing
Disable command-line editing.

--no-site-file
Dont read the site-wide `octaverc file.

--norc
-f
Dont read any of the system or user initialization files at startup. This is equivalent to using both of the options --no-init-file and --no-site-file.

--path path
-p path
Specify the path to search for function files. The value of path specified on the command line will override any value of OCTAVE_PATH found in the environment, but not any commands in the system or user startup files that set the built-in variable LOADPATH.

--silent
--quiet
-q
Dont print the usual greeting and version message at startup.

--traditional
--braindead
Set initial values for user-preference variables to the following values for compatibility with MATLAB.

PS1 = ">> "
PS2 = ""
beep_on_error = true
crash_dumps_octave_core = false
default_save_format = "mat-binary"
fixed_point_format = true
page_screen_output = false
print_empty_dimensions = false
warn_function_name_clash = false

--verbose
-V
Turn on verbose output.

--version
-v
Print the program version number and exit.

file
Execute commands from file.

Octave also includes several built-in variables that contain information about the command line, including the number of arguments and all of the options.

theosim project is used for simulation and compilation for computer scientists.
theosim is a simulation and compilation package of several languages which are of theoretical relevance only (PASCALLI, PASCALLINO and RAM).
I am PARTICIPATING in this project! For further information about it, download the files and read AUTHORS and other documents.
Complete documentation included, too. the distribution contains a directory named "examples" with various good example programs in it !
Installation
# tar xzvf theosim-xxxx.tar.gz
# cd theosim-xxxx
# ./configure --enable-nowarnerror
(you may add --enable-nooptimizing if machine is slow)
# make
# make install
(as root user. will put programs in /usr/local/bin)
Enhancements:
- Released 1.0.17
- Fixed parametercountmismatchbug
- Fixed whilerbug