Distance-based methods are popular for reconstructing evolutionary trees of protein sequences, mainly because of their speed and generality. A number of variants of the classical neighbor-joining (NJ) algorithm have been proposed, as well as a number of methods to estimate protein distances. We here present a large-scale assessment of performance in reconstructing the correct tree topology for the most popular algorithms. The programs BIONJ, FastME, Weighbor, and standard NJ were run using 12 distance estimators, producing 48 tree-building/distance estimation method combinations. These were evaluated on a test set based on real trees taken from 100 Pfam families. Each tree was used to generate multiple sequence alignments with the ROSE program using three evolutionary models. The accuracy of each method was analyzed as a function of both sequence divergence and location in the tree. We found that BIONJ produced the overall best results, although the average accuracy differed little between the tree-building methods (normally less than 1%). A noticeable trend was that FastME performed poorer than the rest on long branches. Weighbor was several orders of magnitude slower than the other programs. Larger differences were observed when using different distance estimators. Protein-adapted Jukes-Cantor and Kimura distance correction produced clearly poorer results than the other methods, even worse than uncorrected distances. We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods.
Research has repeatedly pointed out the suitability of adhesive bonding to substitute to "traditional" joining techniques for numerous materials and loads, including timber to glass. Practitioners, however, are still reluctant to implement them into their designs. Adhesion as a method of joining, particularly in the context of hybrid structures, presupposes knowledge of all involved materials, including codes and procedures; most practitioners however tend to be focused on just a subset of materials. While such specialization is not unusual, it makes it challenging to implement novelty (i.e. new materials or techniques). Additionally, when it comes to adhesion where most of the knowledge has been generated by chemists, the lines become even more blurred. Taking the example of a pedestrian timber-glass bridge, this research shows how design and dimensioning of complex bonded hybrid structures can be performed in accordance with "traditional" engineering practice. The paper guides through every step, from the first concepts to the final design, including the manufacturing, of a relatively complex structure, in which timber and glass act together as equivalent members. The compliance of this process with engineering models is emphasized, and the embedment into existing codes and standards is sought after to ensure acceptancy by practitioners.
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