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Phylogenetic Tree Drawing Application dissertion

Phylogenetic Tree Drawing Application dissertion

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Phylogenetic Tree Drawing Application dissertion

This report explains how a Phylogenetic Tree Drawing Application was designed and implemented by Daniel West under the supervision of Professor Norman Paton during the academic year 2006/2007. It outlines the research, design, what went right, and what went wrong during each stage of the creation of the application. The main part of the report is the research conducted during the project and the development of the data structure to be used to hold the phylogenetic tree. Although there was limited success in meeting the objectives, there were achievements made in the form of lessons learnt from undertaking the project, these have been fully discussed in the report. The conclusion of the report highlights the areas where the project went wrong, where it could be improved, and possibilities on how it could be advanced.

This project was proposed by the Information Management Group (School of Computer Science) and presented by Mike Cornell and Cornelia Hedeler in conjunction with Professor Norman Paton. It was originally proposed that the application take information from the data warehouse within e-Fungi and use the information to build an interactive phylogenetic tree that could be traversed, therefore relating clusters to the tree via graph analysis. The application could then be used in the lab for query logging, viewing protocols and analysing clusters to assist with research purposes.

However, the project was redirected after consultation with Norman Paton, Toby Howard and Ian Pratt-Hartmann with the outcome being that the program should output two different types of trees that use separate mapping algorithms, where the data is loaded from a file.

The Project

This document outlines the process of creating a phylogenetic tree drawing application, explains why the application was proposed and what the objectives of the project were. It starts off by giving a brief overview of what phylogenetic trees and trees in general are. It then continues on to discuss research done on current phylogenetic tree drawing applications currently available for use, and research done on drawing techniques and web technologies. It will then describe the tasks undertaken in designing the application, any user requirements, design objectives, data structures, algorithms that were chosen, and the web technologies to be used. Next it will outline the decision-making processes and what was done during the implementation of the project. It will then interpret what went right and what went wrong during the implementation stage, how the errors were tested, alternative ideas when something went wrong, and gives an analysis of the results when the application was tested. Finally it will give an overall conclusion of what happened in the project, what lessons were learnt and recommendations on how the project could be improved or advanced.

Reasons behind the proposal

The School of Computer Science in conjunction with the Faculty of Life Sciences and University of Exeter have been involved in a research project called e-Fungi [1]. The e-Fungi website states that as part of this research, a data warehouse was developed to integrate data from multiple fungal genomes in a way that facilitates the systematic comparative study of those genomes [1].

The problem with e-Fungi is that there is no way to visually represent the data stored in the warehouse. Therefore, it was proposed that an application should be implemented to take data from e-Fungi and show it as a phylogenetic tree. This can then help the users see which fungi are related and how.

Phylogenetic Tree

A phylogenetic tree is similar to a family tree in that it shows relationships between entities, however a phylogenetic tree shows evolutionary relationships between various species. That is to say, each node with descendants represents the most recent common ancestor of the associated descendants.

Though originally the idea of a tree came from the early thoughts of life to be an advancement from lower to higher forms, modern evolutionists still use them to show evolution as they effectively show the idea that the splitting of lineages is the reason behind the formation of new biological species.

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1 Introduction...................................................... 6
1.1 The Project ....................................................... 6
1.1.1 Reasons behind the proposal ...............................................6
1.1.2 Aims and Objectives .....................................................7
1.2 Phylogenetic Tree .................................................. 7
1.2.1 Types of Phylogenetic Trees ...............................................8
1.2.2 Limitations of Phylogenetic Trees ..........................................10
2 Background..................................................... 11
2.1 Tool Features ..................................................... 11
2.1.1 Branch Swapping .......................................................11
2.1.2 Browsing amongst trees ..................................................11
2.1.3 Collapse and Expand nodes ...............................................11
2.1.4 Draws more than one type tree.............................................11
2.1.5 Interactivity specify areas using the mouse ...................................12
2.1.6 Outputs as WMF files ...................................................12
2.1.7 Outputs as BMP/JPEG/PNG/GIF ..........................................12
2.1.8 Outputs as image map ...................................................12
2.1.9 Outputs to a viewer .....................................................12
2.1.10 Outputs as PDF .......................................................12
2.1.11 Output as Postscript ....................................................12
2.1.12 Reads NEXUS files ....................................................13
2.1.13 Reads PHYLIP files ....................................................13
2.1.14 Roots the tree at node click ..............................................13
2.1.15 Runs on HTTP server...................................................13
2.1.16 Shows bootstrap scores .................................................13
2.1.17 Shows edge labels .....................................................13
2.1.18 Uses C/C++ ..........................................................13
2.1.19 Uses Java ............................................................13
2.1.20 WWW settings require configuration for web applications......................14
2.1.21 Zooming .............................................................14
2.2 Applications ...................................................... 14
2.2.1 Phylodendron ..........................................................14
2.2.2 PhyloDraw ............................................................15
2.2.3 NJPlot................................................................15
2.2.4 TreeView .............................................................16
2.2.5 TreeEdit ..............................................................16
2.2.6 PHY-FI...............................................................17
2.2.7 Bosque ...............................................................18
3 Design ......................................................... 19
3.1 User Requirements ................................................ 19
3.1.1 Design Objectives ......................................................20
3.2 Data Structure .................................................... 20
3.3 Algorithms ....................................................... 22
3.3.1 Radial Layout Algorithm .................................................22
3.3.2 Circular Layout Algorithm................................................24
3.4 Application Features ............................................... 26
3.5 Web Enabling .................................................... 27
3.5.1 Java Servlets...........................................................27
3.5.2 Java Web Start .........................................................27
4 Implementation .................................................. 28
4.1 Data Structure .................................................... 28
4.2 Data Input ....................................................... 28
4.3 Algorithms ....................................................... 29
4.4 Tree Drawing..................................................... 29
5 Testing and Analysis .............................................. 30
5.1 Data Structure .................................................... 30
5.1.1 Using pointers .........................................................30
5.1.2 Using an Arraylist ......................................................31
5.1.3 Using Vectors..........................................................31
5.2 Other methods implemented ........................................ 32
5.2.1 searchTree ............................................................32
5.2.2 addNode ..............................................................32
5.2.3 printTree..............................................................33
5.3 Results Analysis................................................... 33
6 Conclusion...................................................... 34
6.1 Lessons Learnt.................................................... 34
6.2 Project Issues ..................................................... 35
6.3 Improvements .................................................... 35
6.3.1 Reading the tree in from a file .............................................35
6.3.2 Adding another algorithm ................................................35
6.3.3 Generating a graphical tree ...............................................36
6.4 Future advancements .............................................. 36
6.4.1 Interactive Edges and Nodes ..............................................36
6.4.2 Connecting the application to e-Fungi .......................................36
6.4.3 Running the application on the Internet......................................36
6.4.4 Integrating the application to the-Fungi website ...............................37
6.5 Summary ........................................................ 37
7 References ...................................................... 38
Appendix A ........................................................ 39
Appendix B ........................................................ 41
Appendix C ........................................................ 49

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