By Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao (auth.), Ben Raphael, Jijun Tang (eds.)
This publication constitutes the refereed lawsuits of the twelfth foreign Workshop on Algorithms in Bioinformatics, WABI 2012, held in Ljubljana, Slovenia, in September 2012. WABI 2012 is considered one of six workshops which, besides the ecu Symposium on Algorithms (ESA), represent the ALGO annual assembly and makes a speciality of algorithmic advances in bioinformatics, computational biology, and structures biology with a specific emphasis on discrete algorithms and machine-learning equipment that tackle vital difficulties in molecular biology. The 35 complete papers awarded have been conscientiously reviewed and chosen from ninety two submissions. The papers contain algorithms for quite a few organic difficulties together with phylogeny, DNA and RNA sequencing and research, protein constitution, and others.
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Additional info for Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings
We used this to assess the error introduced by randomized estimation of these values, using the full mammal tree and sample sizes of 20, 100 and 500 tips–see Fig. 2. The random method (using 100 draws) produced accurate estimates of the expectation of MPD, but estimates of the standard deviation varied widely around the true 42 C. Tsirogiannis, B. Sandel, and D. Cheliotis value, ranging by as much as 20%. Similar results were found for PDI, but we note that the calculation of the analytical solution for PDI introduces numerical errors, which have an unknown contribution to the ﬁnal estimate.
Dev. 20 100 500 20 100 500 Number of species Fig. 2. Errors introduced in the estimation of NRI and PDI using randomization to estimate the expectation and standard deviation. The heavy line indicates the median error, the box shows the interquartile range, and whiskers show the full error range. 4 Concluding Remarks We described eﬃcient algorithms for the analytical computation of the expectation and the standard deviation of popular measures in phylogeny, namely for MPD and PD. We also provided eﬃcient algorithms for executing individual queries of these meausures on phylogenetic trees.
As mentioned in Remark 2, it seems quite diﬃcult to design, or disprove the existence, of an algorithm with a subquadratic running time for this problem. However, even for large tree sizes and small sample sizes, our algorithm provides better running time, if one uses the standard 1000 random draws rather than 100 as illustrated. Much of the running time for our algorithms for individual MPD and PD queries is spent reading the input tree. 002 seconds and depends weakly on sample size. 4 seconds.
Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings by Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao (auth.), Ben Raphael, Jijun Tang (eds.)