Materials for Assembling the Tree of Life (ATOL)

List by Rod Page

This site contains links to various documents and sites that may be relevant to Tree of Life issues, with an emphasis on "phyloinformatics." This site is not meant to be comprehensive or complete. if you have anything you'd like to add please let me know. Many of the documents listed here are preliminary reports, meeting abstracts, etc.

Contents

  1. Discussion documents
  2. Media
  3. ATOL documents
  4. General issues
  5. TOL databases
  6. Taxonomic names and servers
  7. Phyloinformatics
  8. Tree building methods
  9. Phylogenetic standards and data formats
  10. Software issues and examples

 

Discussion documents [top]

ATOL Phyloinformatics Issues (Rod Page)

Media [top]

Item on BBC Radio 4's "Today" programme, 12 November 2002 [Click to hear MPEG (6 Mb in size), or go direct to BBC Web site for RealPlayer feed]

Vincent Savolainen and Mark W. Chase's letter to Science on "Europe's Fight for the Tree of Life" [local copy]

ATOL Documents [top]

FP6 Expression of interest at CORDIS

Expression of Interest

Executive summary

Report on Kew meeting

General issues [top]

Building a Bioinformatics Nation Lincoln Stein's keynote at O'Reilly's Bioinformatics Technology Conference address (slides available here [or get local copy]). See also his Nature article. Lincoln discusses how to get different databases to talk to each other.
Informatics for 'small' organisms Advice on building model organism databases, much of which is applicable to TOL [local copy].
NSF Tree of Life workshops Local collection of NSF reports on TOL (with links to original sites).
Global Biodiversity Information Facility The purpose of the Global Biodiversity Information Facility (GBIF) is to make the world's biodiversity data freely and universally available.
Towards a global biological information infrastructure Towards a global biological information infrastructure Challenges, opportunities, synergies, and the role of entomology Edited by: H. Saarenmaa and E. S. Nielsen   European Environment Agency Technical Report no 70 [pdf] [local copy]
Bioinformatics for Biodiversity Science magazine's list of sites related to their special issue on biodiversity.
Deep Green Challenges A tradition in the computer science, information technology, and mathematical communities is to issue "challenges." Such challenges pose problems to fellow scientists, and provide an entertaining way to advance the discipline. The Deep Green Challenges apply this idea to phylogenetic reconstruction.

TOL databases (where we are now) [top]

TreeBASE Relational database of trees and datasets
Mary Walsh's essays on TreeBASE Mary Walsh's fascinating site deals with scientific communication, as well as providing insight into the design of TreeBASE.
Tree of Life "A collaborative Internet project containing information about phylogeny and biodiversity"
EMBL-Align EMBL alignment database [see Bioinformatics article]
Taxonomy Workbench Web interface to taxonomy driven queries of sequence databases. See Bioinformatics paper for details.

Taxonomic names and servers [top]

Species2000 Goal is to list all species names
ITIS Database with good query interface.
Species Analyst - Taxonomic Name Service Discussion of some of the issues involved
   

Phyloinformatics [top]

Towards a Visual Query Interface for Phylogenetic Databases Hasan M. Jami, Giovanni A. Modica, Maria A. Teran
PhyloSource: An Interactive Phylogenetic Relationship Repository Dong-Guk Shin 1 , John Blius 1 , Ravi Nori 1 , Hsin-Wei Wang 1 , Pinglei Zhou 1 , and J. Peter Gogarten 2
Joel Cracraft's vision of phyloinformatics  
   

Tree building methods (just a few!) [top]

Quick neighbor joining Build neighbor joining trees for very large (e.g., 27,000 sequences) datasets
Metapopulation genetic Algorithm Lemmon & Milinkovitch's new tree building method
   
   

 

Phylogenetic standards and data formats [top]

Juan Raymundo Iglesias, Gopal Gupta, Enrico Pontelli, Desh Ranjan, Brook Milligan: Interoperability between Bioinformatics Tools: A Logic Programming Approach NEXUS as a tool for communicating bioinformatics information. [local copy]
NEXUS format home page Rather incomplete description of the NEXUS format.
   
   

 

Software issues and examples [top]

Webservices for Bioinformatics Examples of how to get bioinformatics databases and services to communicate with each other
TreeViz Mesquite module to explore trees and tree space
Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions CAVE environment for viewing trees
TreeWiz: interactive exploration of huge trees Java applet for viewing big trees (available here)
H3Viewer The H3Viewer library provides layout and interactive navigation of node-link graphs in 3D hyperbolic space.

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