The Netherlands: Different Set of 30 H5N1 Strains Generated in Tree Format
This suggests there may have been more intermediate steps that we might explore using different hypothetical subsets of 15-50 virii to see what the most-likely phylogeny leading up to them is. But the "k10" subtree confirms an earlier comment by Dr. Niman that the Mongolian and Novobirisk strains are very closely related. The "k11" subtree suggests that there was a transmission of virus between Korea and Japan with those very low numbers. Overall the S(T) score of 0.990241 means that the computer believes it has figured out the structure nearly perfectly. Now it's our job to figure out why.
(Suggestions for better choices of species to try are always welcome.) Rudi stresses that he would love to try more recent data and thinks that this is the most important use for this type of chart at the moment, i.e. to track which strains are going where and when new strains pop up we can match them to the nearest previously known strain in the hope that this can shed light on the epidemiology of the situation.
Rudi has clarified that the data sources for the sequence data and the distance approximation technique (read more about this on the FluWikie) were obtained from a fellow member at the Bird Flu Discussion Forum (AvianFluTalk) whose onlinse pseudonymn is "gs" and it is presumed that 'gs' extracted the data from one of the two Databases at FluWikie. Rudi was trying to determine Normalized Compression Distance, a modern more robust measure than normal multiple alignment like you get from BLAST in certain situations and more information about this is available from Paul Vitanyi on the FluWikie as well as the web or just search for/google Rudi's complete name which has a bunch of papers tagged along with examples. More importantly his measure is a lot easier to operate as it is essentially parameter-free and so is a good choice as a first approximation analysis of a medium to large group of samples of unknown relation.
On a final note, readers are kindly requested to suggest Rudi a better group of 30 samples to use in order to provide and gain more insight (please email your suggestions to cilibrar at ofb.net) to the situation.