Free forests 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

B::Graph is a Perl compiler backend to produce graphs of OP trees.

SYNOPSIS

perl -MO=Graph,-text prog.pl >graph.txt

perl -MO=Graph,-vcg prog.pl >graph.vcg
xvcg graph.vcg

perl -MO=Graph,-dot prog.pl | dot -Tps >graph.ps

This module is a backend to the perl compiler (B::*) which, instead of outputting bytecode or C based on perls compiled version of a program, writes descriptions in graph-description languages specifying graphs that show the programs structure. It currently generates descriptions for the VCG tool (http://www.cs.uni-sb.de/RW/users/sander/html/gsvcg1.html) and Dot (part of the graph visualization toolkit from AT&T: http://www.research.att.com/sw/tools/graphviz/). It also can produce plain text output (which is more useful for debugging the module itself than anything else, though you might be able to make cut the nodes out and make a mobile or something similar).

OPTIONS

Like any other compiler backend, this module needs to be invoked using the O module to run correctly:

perl -MO=Graph,-opt,-opt,-opt program.pl
OR
perl -MO=Graph,-opt,obj -e BEGIN {$obj = ["hi"]}; print $obj
OR EVEN
perl -e use O qw(Graph -opt obj obj); print "hi!n";

Obj is the name of a perl variable whose contents will be examined. It cant be a my() variable, and it shouldnt have a prefix symbol ($@^*), though you can specify a package -- the name will be used to look up a GV, whose various fields will lead to the scalar, array, and other values that correspond to the named variable. If no object is specified, the whole main program, including the CV that points to its pad, will be displayed.

Each of the the opts can come from one of the following (each set is mutually exclusive; case and underscores are insignificant):

-text, -vcg, -dot

Produce output of the appropriate type. The default is -text, which isnt useful for much of anything (it does draw some nice ASCII boxes, though).

-addrs, -no_addrs

Each of the nodes on the graph produced corresponds to a C structure that has an address and includes pointers to other structures. The module uses these addresses to decide how to draw edges, but it makes the graph more compact if they arent printed. The default is -no_addrs.

-compile_order, -run_order

The collection of OPs that perl compiles a script into has two different layers of structure. It has a tree structure which corresponds roughly to the synactic nesting of constructs in the source text, and a roughly linked-list representation, essentially a postorder traversal of this tree, which is used at runtime to decide what to do next. The graph can be drawn to emphasize one structure or the other. The former, compile_order, is the default, as it tends to lead to graphs with aspect ratios close to those of standard paper.

-SVs, -no_SVs

If OPs represent a programs compiled code, SVs represent its data. This includes literal numbers and strings (IVs, NVs, PVs, PVIVs, and PVNVs), regular arrays, hashes, and references (AVs, HVs, and RVs), but also the structures that correspond to individual variables (special HVs for symbol tables and GVs to represent values within them, and special AVs that hold my() variables (as well as compiler temporaries)), structures that keep track of code (CVs), and a variety of others. The default is to display all these too, to give a complete picture, but if you arent in a holistic mood, you can make them disappear.

-ellipses, -rhombs

The module tries to give the nodes representing SVs a different shape from those of OPs. OPs are usually rectangular, so two obvious shapes for SVs are ellipses and rhombuses (stretched diamonds). This option currently only makes a difference for VCG (ellipse is the default).

-stashes, -no_stashes

The hashes that perl uses to represent symbol tables are called stashes. Since every GV has a pointer back to its stash, its virtually inevitable for the links in a graph to lead to the main stash. Unfortunately stashes, especially the main one, can be quite big, and lead to forests of other structures -- theres one GV and another SV for each magic variable, plus all of @INC and %ENV, and so on. To prevent information overload, then, the display of stashes is disabled by default.

-fileGVs, -no_fileGVs

Another kind graph element that can be annoying are the pointers from every GV and COP (a kind of OP that occurs for every statement) to the GV that represents the file from which that code came (used for error messages). By default, these links arent shown, to keep them from cluttering the graph. Also, perls internal interfaces changed in a recent version, so in perl 5.005_63 or later you cant see the fileGVs at all.

-SEQs, -no_SEQs

As it is visited in the peephole optimization phase, each OP gets a sequence number, which is currently used by anything (except the peephole optimizer, to avoid visiting OPs twice). If you want to see these, ask for them. (COPs have their own sequence numbers too, but theyre more interesting to look at -- for instance, theyre used to bound the lifetimes of lexicals).

-types, -no_types

B::Graph always gives the type of each OP symbolically (entersub), but it can also print the numeric value of the type field, if you want. The default is no_types.

-float, -no_float

Almost every OP has an op_next and an op_sibling pointer, and B::Graph colors them distinctively (pink and light blue, respectively). Because of this, it isnt strictly necessary to anchor the arrow on a line in the OPs box saying op_next. The float option lets the graph layout engine start these arrows wherever it wants, which can sometimes lead to a more pleasing layout, at the expense of being less obvious. The default is not to float.

-targlinks, -no_targlinks

Lexical (my()) variables and temporary values used by individual OPs are stored in pads, per-code arrays linked to the CV. OPs store indexes into these arrays in the op_targ field, but B::Graph can often also draw links directly from the OP to the SV that stores the name of the variable. These links dont correspond to any real pointers, however, and they can make the graph more complicated, so they are disabled by default.

Faerion IRC Server project consists of an advanced, secure, multi-lingual IRC server for Unix/Win32.
Faerion is a Unicode-based IRC server. It features enhanced support and transparent conversion for different charsets, and provides a stealth network model, persistent channels, compressed links, etc.
Main features:
- Support for transparent, user-controlled charset translation (virtually) from anything to anything. This is done by using Unicode mappings, which can be installed or removed on the fly, without having to interrupt the server. The server supports a special "fallback" conversion table which maps all characters that are not supported by a users preferred charset to the closest looking characters. This process is typically referred to as "transliteration" and is widely used on Russian IRC networks to avoid problems with incompatible charsets. The difference is that with Faerion, the server takes all necessary investigation to see what should be transliterated, and what can be passed without changes.
- Clients that have native support for Unicode (UTF-8), will benefit from using it at full scale without the implication of "cryptic writings" (which raw UTF-8 is for a typical human eye).
- Support for "persistent channels": channels registered with the Channel Service (mode +r) are not deleted when the last user leaves. This slightly saves bandwidth and helps mitigate several privacy issues (such as channel key revelation).
- Support for channel forwarding based on user address matching rules: with channel mode +f enabled, all ban masks can have a ",#channel" suffix appended to them to forward clients to another channel instead of declining the attempt to join the channel.
- Limited portability. The server is currently available for most POSIX platforms (modern BSD and Linux variants) and Microsoft Windows.
Enhancements:
- The LIST command now requires users with unregistered nicknames to additionally specify a pseudo random number to prove their human nature, otherwise the command is ignored.
- Opers no longer need an O-line to use any command; remotely set +o works just fine.
- Fixed the charset conversion problem when a user gets registered on the server.
- Invite list no longer overrides ban list.
- Fixed a crash in WHOIS.
- Fixed to compile without warnings in -Werror mode with GCC 3+.
- Fixed the +c channel mode to disallow colors instead of stripping them.Also, when a topic is being changed by a nonop on a +c-t channel to something that contains colors, the attempt is denied.

Vallheru is a turn-based, fantasy MMORPG written in PHP and MySQL (but may work with many other databases) with Smarty Template Engine, ADOdb, and PHP Mailer.
It is based on Gamers-Fusion 2.5 with many modifications in security, speed, and features. Vallheru is currently available only in Polish.
Whats New in 1.3 Beta Development Release:
- This version contains many changes in the game interface making it simpler to mine and explore forests and mountains.
- Some new features were added, such as the ability for players to add their own links to the menu and to report bugs while in the game.
- Additionally, this release has a new quest, a few changes in game mechanics (especially alchemy and mage items and spells).
- For administrators, some security and normal bugs were fixed, some code optimization was done, and new versions of third-party software are used.
Whats New in 1.0.9 Stable Release:
- BUG,train.php: fixed bug with train condition
- BUG,languages/pl/checkexp.php: fixed bug in text
- BUG,landfill.php, bank.php, outposts.php, tribes.php, house.php, tribearmor.php, tribeware.php, includes/head.php: fixed possible integer overflow

cadaverserver project is a realtime artificial intelligence battle game server.

Cadaver is a simulated world of cyborgs and nature in realtime. The battlefield consists of forests, grain, water, grass, carcass (of course) and lots of other things.

The game server manages the game and the rules. You start a server and connect some clients. The clients communicate with the server using a very primitive protocol. They can order cyborgs to harvest grain, attack enemies or cut forest.

The game is not intended to be played by humans! Instead the idea is that you write artificial intelligence clients to beat the other artificial intelligences.

The server is a program that runs on the console.
It manages the rules of the game in realtime.

It listens on TCP port 8932.

You could connect to it by entering:

# telnet localhost 8932

You will get the Initialisation message.
You can now enter commands.

SuperTux project is a classic 2D jumpn run sidescroller game in a style similar to the original SuperMario games. The Milestone1 release of SuperTux features 9 enemies, 26 playable levels, software and OpenGL rendering modes, configurable joystick and keyboard input, new music and completly redone graphics.
Together with a little story, we hope to provide a good gaming experince with this first Milestone release.
The improvments in Milestone1 are in huge part the result of the work done surrounding the Game of the Month March 2004 event on happypenguin.org.
The Milestone1 section of this webpage was mainly used to coordinate development and to post sketches and other things. It will give you an overview of the development of the features and enemies that have gone in Milestone1, it might be a bit outdated and is mainly present for historic reasons to those interested in the development.
Enhancements:
- new, OpenGL- and OpenAL-based engine
- final boss for Icy Island
- brand new Forest World with new badguys and new game objects
- new and improved soundtrack, immersive sound effects
- much more...

Lynns Legacy is an action-adventure game. Lynn the mercenary is on a quest to figure who tried to kill her and why.

Follow Lynn the mercenary as she recollects the mysterious mission that nearly took her life. Travel through multiple overworld areas, (forest, towns, desert, mountains) and boldly step into uncharted dimensions in search of memory!