[Taxacom] Phylogeny browser for APGII and the Western Australian flora

[Chapman, Alex]

Thanks to the various correspondents who pointed out the 'letterbox view' of the applet window in certain web browsers.
 
After protracted head-scratching on my part, FloraBase colleague Ben Richardson has nutted out the (frustratingly subtle) reason for this discrepancy in functionality between browsers.  We have released a new version of FloraBase which, amongst other improvements, allows the Phylogeny Browser to work exactly the same in a much broader range of modern browsers, including IE 6, Firefox 1.5 and Opera 8.5.

Note that data anomalies still exist for a proportion of the external links in the database.  These are largely attributable to the fact that I have automated the linkage from the APGII data (usually by order name), rather than fully customise links to external sites based on their internal organisational structure.  I will try and minimise these issues over the next few weeks.
 
The Phylogeny Browser does require the (free) Java Runtime Engine to be installed; a link is available on this page: http://florabase.calm.wa.gov.au/phylogeny/ <http://florabase.calm.wa.gov.au/phylogeny/> .

Alex
 
________________________________

From: Chapman, Alex
Sent: Mon 18/09/2006 9:03 AM
To: 'taxacom at mailman.nhm.ku.edu'
Cc: Herbarium All Users
Subject: Phylogeny browser for APGII and the Western Australian flora


A demonstration of the potential for interactive phylogeny browsers has recently been published on FloraBase - the Flora of Western Australia at http://florabase.calm.wa.gov.au/phylogeny/ <http://florabase.calm.wa.gov.au/phylogeny/>  .
 
The Phylogeny Browser provides the user with a view of the higher-level relationship of all plant orders and families, and indicating those occurring in Western Australia. It uses interactive cladograms which integrate with plant family content elsewhere in FloraBase, and with other web resources. Once loaded, they also link to further cladograms for the lower plants, which indicate the relative placement of the bryophytes, algae, fungi and lichens in the 'tree of life'.
 
First demonstrated at an NSF-funded workshop in Gainesville Florida in 2004, the browser differs from many visual tools presenting higher-level phylogenetic concepts in linking deeply into maintained database content, allowing the user to browse through the APGII tree and drill right down to current species and even specimen-level information for a botanically significant region comprising some 3% of the world's angiosperm flora.
 
Such a tool is useful for a number of user groups, not least the local tertiary education sector, allowing the WA flora to be readily perceived in context with related families from around the globe, with external links out to the Tree of Life, Angiosperm Phylogeny Web and Families of Flowering Plants sites.  It also goes some way to integrating herbarium collections management (often maintained in an aging classificatory sequence) with recent phylogenetic hypotheses.
 
Note that the data driving the Browser is derived exclusively from the APGII publication (APGII, 2003) and does not cater for subsequent phylogenetic hypotheses published elsewhere. This is intentional, providing a stable reference point until further collaborative statements on the angiosperms are generated.  Inevitably, changes to the structure, filenames or content on the external sites linked to by the Browser may cause certain links to fail, or return unexpected data. 

____ 
Alex R. Chapman                    Email: alexc at dec.wa.gov.au 
FloraBase Manager             http://florabase.calm.wa.gov.au <http://florabase.calm.wa.gov.au/>  
Research Scientist           Voice/Fax: +61 8 9334 0513 /0515 
WA Herbarium   -   Department of Environment and Conservation 
Locked Bag 104 Bentley Delivery Centre Western Australia 6983