TreeDyn Crack

TreeDyn is an open source library and application for displaying tree representations in SVG.

In contrast to the basic newick format, where all the information is part of the tree itself, TreeDyn allows the user to incorporate a list of information that is not part of the tree into the tree itself, like user-defined variables, comments or a list of taxonomic names.

TreeDyn has been developed since more than 5 years and has recently been upgraded to 2.0 (last version 1.1.0 of 2013). The main addition is the creation of the improved graphics operators, which are fully backward compatible with the old one.

TreeDyn 2.0 now supports:

SVG graphics

The library offers a SVG API that uses the element to display the tree.

This new API should reduce the bottleneck in display time compared to the old one (displayed in newick format) and support graphic filtering through new graphics options: font size, and opacity.

Also, the new API provides a unified rendering of multiple SVG graphics, making it possible to combine them, e.g. SVG graphics of an interactive map and a tree map.

It is now possible to change the tree’s displayed graphic to highlight new nodes that are found.

You can now “freeze” the tree by enlarging only a few elements of the tree (e.g. for showing the search path of the tree). This is useful if, for instance, the tree shows phylogenetic relationships, and one wants to zoom in on a very close species to analyse it.

TreeDyn 2.0 also provides a new API for the dynamic creation of SVG graphics, which makes it possible to integrate newly created graphics into the tree. This makes it possible to do partial analyses of the tree, or just to display a new part of the tree.

Web graphics (more efficient)

The previous version used the newick format to display the tree graphics. Because of the large size of many trees, the user had to wait a long time to load the tree image, and even to scroll the image.

The SVG API implemented a new rendering that is a lot more efficient. The size of the tree is now reduced by at least 40% compared to the previous one.

At the same time, the SVG graphics are now created “on demand”. Only the parts of the tree that are displayed are created on demand.

– The VARIABLES and VALUES macros can be used to define new sub-variables/values pairs of meta-information. The VALUES macro is used to define leaves’ labels, with 3 parameters :
– the new macro is declared by using the VARIABLES macro
– the leaf’s identifier is passed to the VALUES macro
– the value (or the label) is set using the VALUES macro
– the leaf identifier is defined using the VARIABLES macro
Example of a VARIABLES definition:
VARIABLES ( ‘w’ w v ‘@’ a ( ‘@’ b, c ) )

The macro VALUES is a list of nodes’ identifiers.
Example of a VALUES definition:
VALUES ( ‘a’, ‘b’, ‘c’ )

In dynamic graphics applications, variables are created on-the-fly. A variable is created for every labels of each node of the tree.

The labels of nodes are stored in a variable called varLabel. The initial value of varLabel is set to “label”.

The labels of leaves are stored in a variable called varValue.

A representation of this variable is the following data structure:
{ ‘a’, [ ‘b’, ‘c’ ], ‘label’ }

The structure is identical to the list [a, b, c] except that the value of a node identifier is replaced by its label and no parenthesis are used.

Newick (short for Newick notation) is a universal format for the description and exchange of phylogenetic trees. It is an ASCII-based representation of a tree, with a distinct encoding for each character. This allows any client to read, manipulate, and write Newick. The format is simple to work with, compact and elegant.

Newick’s syntax is based on 4 basic elements: nodes, edges, labels, and pointers. In Newick, a leaf is always labeled.

In this example, we give the Newick description of a phylogenetic tree including 3 species: 1 human and 2 primates. A pointer to the phylogenetic tree is included, and the edge lengths are set to 1.

To view a Newick tree, the user must be connected to the server via the bio.io.newick2newick.serve_root_url script in the BioPython package’s test directory.
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TreeDyn is a complete and open source framework to produce, interact with and analyse tree graphics.

It includes:
An XML editor allowing to easily manipulate existing data (in our case the meta-information information of the trees) and submit them to the framework
A tree viewer, allowing to interactively browse tree file formats (The newick format, MTL format or HTML format) and show the relationship between the leafs of the tree and the associated meta-information.
A tree graphic builder, allowing to display the resulting graphics in several formats: as a JPEG image, as SVG (Scalable Vector Graphics) or as PDF
A tree graph builder, allowing to produce interactive graph views where nodes and edges can be dragged and dropped
A tree annotation manager, allowing to define an arbitrary set of leaf labels, and to associate these leafs to any additional metadata.
A tree annotation editor, allowing to edit existing annotations within the framework and then submit them to the graphical operators to update the images
An information visualization framework using dynamic graphics and various information visualization tools (Projection, Localization, Labelization, Reflection,…).

See also
BioDendro

External links

Category:Free graphics software
Category:Open source biodiversity software
Category:Free bioinformatics software
Category:Bioinformatics software
Category:Hierarchical data structuresToilet Readys For Launch

The clock’s ticking. In three weeks, NASA’s Destiny module will blast off in the space shuttle Atlantis in what will be the second flight of Atlantis since the Columbia disaster. But while the crew’s in training for the long launch, they’ve been worrying about the same thing everyone else has been worrying about: Which toilet to use on the mission.

The problem is that water is an essential part of doing business in space. But when you’re several billion miles from Earth, there’s no way to send a replacement. So the crew has had to make do with water that’s already out there. And if they use any of it, there’s a chance they could be stuck on a space toilet until their return.

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TreeDyn is a free open source Java application providing a solution to the challenge of the mapping between unique tree leaf labels and lists of variables/values pairs of annotations (meta-information).

Its development started in 1998 to provide an easy and direct interface for the common task of displaying tree structures and their meta-information. It grew since then to cover numerous tree visualisation and information visualisation needs, including newick parsers, reformatting of trees, MEGA2-format parsing, and intermediate formatting for html, pdf or postscript.

Latest features
Integrates with the MEGA2 package.

Contributors:
A. Antunes, F. Tissot, B. Chevallier, D. Lévesque, J. Berry, B. Carrière, M. Grosjean, P. Vandepas, P. Parise, P. Grosjean, R. Stamm, C. Lassalle, M. Dufour, R. Roux, R. Chauret, N. Bordage, J. Armand-Ugoret, G. Lainé

Website:

Supported Operating Systems:
Java SE 6, 7 and 8
Mac OS X 10.7 and 10.8

Compatibility with trees converted from the newick format:
v.2.0.0, v.1.3.0

License:
GPL2.0

Credits

Sponsor:
CERN, CNRS, the French Research Federation for Particle Physics

Bug reports

Please contact the project’s maintenance coordinator.

See also:
TreeDyn,
MEGA2,
GDV Java library,
Leaflet.js library,
Google Chart API,
PDFBox library
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Minimum:
OS: XP SP3; Vista SP2 or Windows 7.
Processor: Dual-Core 2.0 GHz.
Memory: 2 GB RAM.
Hard Disk: 8 GB free space.
Graphics: DirectX 9.0 Compatible Video Card with support for Pixel Shader 3.0.
DirectX: Version 9.0.
Sound: DirectX compatible sound card with Windows Multimedia Subsystem.
Additional Notes:
How To Install:
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