Yggdrasill Files

Yggdrasill 0.4.0 Copyright (C) 2016 Philipp Gnoyke


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Description
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# Yggdrasill is a 3D phylogenetic tree visualization software based on the Unity 5 engine. It is intended for educational and scientific purposes and is published under an open source license. Being in its alpha phase, this release allows to display the evolutionary relationships between different tetrapod species.

# Currently available features include procedural tree generation of evolutionary data provided by the Tree of Life (ToL) web project (http://tolweb.org/tree/), full three dimensional camera controls as well as basic interactions with the graphical tree object.

# Later updates will allow for an exploration of the full ToL dataset and include in general various UI improvements, e.g. a search function, potentially the option to display other available data and more. 




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Acknowledgments
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# I would like to thank the Tree of Life Web Project and all its contributors for collecting, maintaining and publishing the phylogenetic data this software is based on. Without the actual scientific foundation this tool could not exist. While being far, far from complete (or in a scientific sense 'correct'), the database lists a multitude of species this planet gave rise to. If you would like to contribute to it, please refer to their website and help to fill in any missing pillar in the cathedral of evolution.

# I also want to thank Unity Technologies and indeed Microsoft for providing open access to all the tools necessary to create this program.




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Controls
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# Camera Controls

	W			forwards
	A			left
	S			backwards
	D			right
	Space			up
	Shift			down
	Right Mouse Button	hold to rotate
	Backspace 		reset
	Mouse Wheel Up		increase camera speed
	Mouse Wheel Down	decrease camera speed

# Node Controls

	Left Mouse Button	select node
	F			focus on selected node
	I			Google search
	C			clear selection
	E			extinct species overlay

# General

	Esc			quit








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Changelog
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### Version 0.4.0 ###

# Graphical optimization update. Added Level of Detail with three custom levels and Baked Lighting, greatly increasing performance with larger datasets.

# Baked Lighting uses an instantiation workaround, as the Unity 5 baked lighting system is not intended for procedural generation during runtime.

# Data is now loaded and processed in a coroutine. The loading screen is now fully functional.

# Implemented a workaround in case the Jarvis march did not filter collinear hull points, which caused an exception in the subsequent circle center calculation.

# Fixed an issue in the enclosing circles approach where branches with a single child would incorrectly refer to the childs center.

# Adjustments to tree and camera parameters.

# Switched displayed ToL data to the larger tetrapods (terrestrial vertebrates) dataset.




### Version 0.3.1 ###

# Improved the tree generation using enclosing circles by implementing the Skyum algorithm.

# In this method the branch's circles are represented by a point set, which is then reduced to the convex hull by a Jarvis march.

# For the resulting hull the Skyum algorithm finds the exact smallest enclosing circle.

# Added a custom Gaussian solver.




### Version 0.3.0 ###

# Implemented a second branch placing approach using enclosing circles. It can be activated optionally in the main menu.

# The method used is close to Ritter's algorithm, it is efficient yet inaccurate. Future releases will implement an exact solver.

# Tweaked the scale of branches and stems.

# Nodes are now offset closer to their parent node.

# Added an option to adjust camera translation speed via buttons and mouse wheel.

# Obligatory changes to the title screen.




### Version 0.2.2 ###

# Another interim update while refining the new circular tree generation pattern (already added in code, but not applied).

# Improved the CornerAlignment method further by removing restrictions for shifting and centralizing shifted blocks.




### Version 0.2.1 ###

# Interim update while working on a new circular tree generation pattern. 

# Improved the CornerAlignment method with additional shifting logic, potentially halfing overall tree extent.

# Camera starting and reset position is now focussed on the tree root.

# Various changes to the splash screen.




### Version 0.2.0 ###

# UI update. Added a splash screen, a main menu as well as a controls overview and navigation buttons in the treeview.

# Treeview now displays ToL mammal data.

# Added a basic loading screen to the Treeview (Not noticable, because of fast loading speed in current version).

# An overlay indicating extinct species can now be toggled.

# Fixed a bug where nodes would not be drawn because of a zero Vector3 argument passed to Quaternion.LookRotation.

# Upgraded project to Unity 5.3.4f1




### Version 0.1.0 ###

# First release version, intended as a demonstration of core features of an upcoming full release.

# Allows to procedurally generate a graphical tree representing the embedded ToL primate data.

# Aside from full camera control it also offers the option to select a node and start a web search for the respective species.