Friday, July 11, 2014

Touching the Data, report 2

We have now completed the workshop.

Since the first report, we have had three more talks. First, Mukul Bansal outlined the relationship between phylogenetic networks and reconciliation analysis, and the way in which the latter can be used to construct the former. Starting from an estimated species tree, the tree for each locus is optimized for fit to the species tree, which helps locate any areas of extensive gene flow (ie. reticulation). This can be done using a large number of loci and an even larger number of taxa.

Celine Scornavacca provided details of some of the fundamental limitations of network analysis.The most important of these is unidentifiability of network topologies -- there are classes of network topologies that cannot be distinguished based on the information that is currently used, so that we cannot guarantee that a unique optimal network will be found during an analysis. Branch lengths may help with this situation, but cannot guarantee to resolve it.

Jim Whitfield covered the advantages and potential problems of using genomic-scale data for phylogenetic analysis. The basic problem is the increased scope for error in moving to the genome data (genome assembly problems, gene homology issues, alignment difficulties), although the potential advantages are extensive.

Most importantly, we spent two days "touching" some data. The participants broke into smaller groups of continuously varying size, each of which focussed on a particular dataset (as supplied by some of the participants). These data were evaluated in many different ways, to assess the characteristics of the data as well as to evaluate the data-analysis methods. This not only allowed us to identify the current state of the art with respect to phylogenetic networks, but it also allowed computationalists to improve their understanding of biological data and how biologists proceed to analyze it, as well as allowing biologists to obtain immediate feedback with respect to their data-analysis issues.

Production of phylogenetic networks seems to have come a long way in the past few years, although there is still no single "one-stop shopping" software tool to use. Practical issues getting programs to perform on all computer types were identified, along with data-format issues. Nevertheless, all of the participants seemed to find that this was a very valuable exercise, as a means of focussing interactions among themselves.

Finally, we considered both European and U.S. funding for network research, in the latter case assisted by David Mindell (from the N.S.F.). In particular, we identified sources of funding for future workshops (either in the south of France or the north-eastern U.S.A.).

The canal-boat cruise turned out well, in spite of the somewhat uncooperative weather. The football, of course, has turned out to be rather disappointing for the hosts, although they have one more game to play.

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