Friday, October 19, 2012

The Future of Phylogenetic Networks: Day 4

There were two talks today and two lengthy discussion sessions.

Hans-Jurgen Badlet started the day with a smallish audience that increased as time progressed. This may have something to do with the noise emenating from the hotel bar the previous night. Hans surveyed the field of splits networks, and especially their uses for data quality control in forensic and medical databases. The extent of this use was news to most of the audience.

The morning discussion turned out to be about the extent to which it might or might not be desirable to have some sort of "standards" or even "protocols" for effective use of network techniques. Clearly, many if not most users of phylogenetics are not experts, and misuse or misunderstanding of networks is a real possibility. There was no particular consensus on this issue.

The afternoon discussions covered three topics. First, we discussed ways of detecting hybridization using networks, as opposed to detecting them using directly biological techniques. There were arguments both for and against the successful use of networks, with the consensus being that networks have a useful role.

We then proceeded to a consideration of the extent to which network methodology is prepared for the expected influx of genome-scale datasets. The answer seems to be "not yet", but even with the available methods there is much scope for effective analysis.

The third topic was the practical use of current methods and programs for exploratory analysis of multi-gene data. A number of additions or modifications to current implementations were suggested, including some measure of "tree-likeness" to rank different genes in terms of their data patterns.

The day finished with Charles Semple, who is always first to breakfast and last to leave. He explained the various measures optimizing the process of combining trees, notably reticulation number and its various definitions. There was much use of the whiteboard, which is the mark of a true mathematician.

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