ASBS ASBS Workshop on Historical Associations

by Dr Rod Page (r.page@bio.gla.ac.uk)
Caley Seminar Room, Royal Botanic Gardens Sydney, Sydney, Australia
8-9 June 2000

Last updated 3 June 2000

This Web site provides background material, course notes, and links for the workshop. Further material will be added prior to the course starting. Any feedback on this site, and the course itself, would be welcome.


The workshop covers the topic of "Historical Associations", which includes gene trees and species trees, host-parasite cospeciation, and biogeography. The workshop is taken from on a larger course run at Glasgow in 1997 (but with additional examples with a more botanical flavour), and will feature the programs GeneTree, TreeMap, and COMPONENT. It is hoped that a test version of TreeMap 2 (featuring "jungles") will be available in time for the workshop. There will also be the opportunity to see and/or use other phylogenetic software developed at Glasgow, such as Spectrum, NDE (Nexus Data Editor),Circles, and Abacus.

For any enquiries regarding the venue, registration, etc. please contact Dr Peter Weston. All enquries regarding content of the workshop please contact Dr Rod Page (r.page@bio.gla.ac.uk).

Requirements

All participants must bring their own computer, either a PC running Windows 95/98/NT, or a PowerMac running MacOS 7.5 or later. Nearly all the programs will run under either operating system.You can download most of the programs before the start of the workshop from Rod Page's home page. In some cases newer or experimental versions wil be available at the workshop. Sample data sets will be supplied, but feel free to bring your own. You may find it useful to have access to a copy of PAUP if you want to investigate some datasets further.

Downloads

You will need the programs GeneTree, TreeMap, and COMPONENT. You may also find TreeView to be useful. These programs can be downloaded from Rod Page's home page. If you have a Mac then you will not be able to use COMPONENT unless you have a PC emulator such as virtual PC. However, most of the analyses can be done using GeneTree. If you don't have a copy of COMPONENT then for the duration of the workshop a copy can be downloaded from here.

Each session has its own page with links to software and example files. You can download all the examples (other than those that come with the software) in one go, if you prefer:

All example files as a Macintosh self extracting archive

All example files as a Zip file

Preliminary program

Each day will be divided into a morning and afternoon session, and each session will start with a lecture or discussion, followed by hand-on use of the software. The final session of Friday afternoon will serve as an opportunity to discuss the topics covered in the workshop, explore your own data, or see demonstrations of other software developed at Glasgow.

Follow a link below to get the relevant software, example files, and course notes.

Thursday 8th June

Morning

Overview of historical associations

Gene trees and species trees

Afternoon

Host-parasite coevolution

TreeMap (and maybe jungles)

Friday 9th June

Morning

Biogeography, problems and prospects

COMPONENT analysis

Afternoon

Review

Other topics, including own data sets, plus demos of spectral analysis, NDE, Circles (RNA structure analysis), Abacus (sequence alignment editor)

 

Background reading

Order from Amazon.com
Rod Page's reprints are available online in PDF format, and all the software comes with at least some documentation. You may also find the recent book by Page and Holmes to be useful (yes, this is a shameless plug).

[Rod Page's home page]